From fcbdd0ece0f38ad6135dfe35246bb98f474529f8 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Tue, 11 Aug 2026 13:30:57 +0200 Subject: [PATCH 1/6] Add a controlled `topics` vocabulary alongside free-form tags MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit `tags` is currently asked to do two jobs with opposite requirements. The website uses it to build the filter row on scverse.org/packages, which needs a small, stable, coherent vocabulary; it is also the only thing making packages findable by keyword, which needs the opposite — breadth, and a long tail nobody has to spell the same way. Serving both from one free-form field means neither works. Across 118 packages there are 259 distinct tags, 71% of them used exactly once. `single cell` and `single-cell` are separate entries, as are three spellings of spatial omics, so the filter row shows the same concept several times and pads the remainder with `python`. The website has been papering over this with a hardcoded alias map, which is invisible to the people writing the tags and silently rots as new packages arrive. Split the two jobs. `topics` is a required, closed vocabulary of 18 terms that says what a package is for, and drives the website filters. `tags` keeps its current meaning, stays free-form, and is used for search, where incoherence is harmless. Topics for the existing 118 packages were seeded from their descriptions and tags, then corrected package by package: the seeding read "annotated data matrices" as annotation, "integration testing" as integration, and missed cellxgene being a viewer. Enforcement needs no new code. `validate_registry.py` already runs `jsonschema.validate` per package, and an unknown topic produces "'foo' is not one of [...]", so contributors get the whole vocabulary at the point where they are blocked. --- README.md | 37 ++++++++++++++++++++++ packages/AESTETIK/meta.yaml | 4 +++ packages/CellAnnotator/meta.yaml | 2 ++ packages/CellCharter/meta.yaml | 4 +++ packages/CellMapper/meta.yaml | 3 ++ packages/CellOracle/meta.yaml | 4 +++ packages/CellRank/meta.yaml | 2 ++ packages/Cell_BLAST/meta.yaml | 2 ++ packages/CellphoneDB/meta.yaml | 2 ++ packages/Cirrocumulus/meta.yaml | 2 ++ packages/DOTools_py/meta.yaml | 2 ++ packages/DRVI/meta.yaml | 2 ++ packages/DoubletDetection/meta.yaml | 2 ++ packages/GPTBioInsightor/meta.yaml | 2 ++ packages/GRnnData/meta.yaml | 3 ++ packages/LazySlide/meta.yaml | 3 ++ packages/Mowgli/meta.yaml | 3 ++ packages/Multivelo/meta.yaml | 3 ++ packages/PEAKQC/meta.yaml | 3 ++ packages/PILOT/meta.yaml | 3 ++ packages/ParTIpy/meta.yaml | 3 ++ packages/PathML/meta.yaml | 2 ++ packages/PyDESeq2/meta.yaml | 2 ++ packages/Rectangle/meta.yaml | 2 ++ packages/SC2Spa/meta.yaml | 3 ++ packages/SCALEX/meta.yaml | 3 ++ packages/STMiner/meta.yaml | 2 ++ packages/SnapATAC2/meta.yaml | 4 +++ packages/TreeData/meta.yaml | 3 ++ packages/alphapepttools/meta.yaml | 3 ++ packages/anndata-for-R/meta.yaml | 2 ++ packages/anndata/meta.yaml | 2 ++ packages/anndataR/meta.yaml | 2 ++ packages/annsel/meta.yaml | 2 ++ packages/benGRN/meta.yaml | 2 ++ packages/bento-tools/meta.yaml | 2 ++ packages/biolord/meta.yaml | 3 ++ packages/cell2location/meta.yaml | 3 ++ packages/cellxgene/meta.yaml | 3 ++ packages/clone2vec/meta.yaml | 2 ++ packages/cookiecutter-scverse/meta.yaml | 2 ++ packages/dandelion/meta.yaml | 3 ++ packages/decoupler/meta.yaml | 2 ++ packages/delnx/meta.yaml | 2 ++ packages/dvp-io/meta.yaml | 4 +++ packages/dynamo-release/meta.yaml | 3 ++ packages/ecosystem-packages/meta.yaml | 2 ++ packages/epiScanpy/meta.yaml | 2 ++ packages/eschr/meta.yaml | 2 ++ packages/favapy/meta.yaml | 2 ++ packages/flashdeconv/meta.yaml | 3 ++ packages/flowsom/meta.yaml | 4 +++ packages/governance/meta.yaml | 2 ++ packages/grassp/meta.yaml | 3 ++ packages/gssnng/meta.yaml | 2 ++ packages/hotspot/meta.yaml | 2 ++ packages/illico/meta.yaml | 2 ++ packages/infercnvpy/meta.yaml | 2 ++ packages/integration-testing/meta.yaml | 2 ++ packages/kompot/meta.yaml | 2 ++ packages/liana/meta.yaml | 3 ++ packages/maxspin/meta.yaml | 3 ++ packages/moscot/meta.yaml | 4 +++ packages/mudata/meta.yaml | 3 ++ packages/muon/meta.yaml | 4 +++ packages/nichepca/meta.yaml | 3 ++ packages/novae/meta.yaml | 4 +++ packages/omicverse/meta.yaml | 2 ++ packages/palantir/meta.yaml | 2 ++ packages/panpipes/meta.yaml | 3 ++ packages/pcdl/meta.yaml | 2 ++ packages/pegasus/meta.yaml | 4 +++ packages/pertpy/meta.yaml | 3 ++ packages/popV/meta.yaml | 3 ++ packages/pyCrossTalkeR/meta.yaml | 3 ++ packages/pyLemur/meta.yaml | 2 ++ packages/pySCENIC/meta.yaml | 3 ++ packages/pyUCell/meta.yaml | 2 ++ packages/pycea/meta.yaml | 3 ++ packages/pychromVAR/meta.yaml | 2 ++ packages/pytximport/meta.yaml | 2 ++ packages/rapids-singlecell/meta.yaml | 3 ++ packages/scCellFie/meta.yaml | 4 +++ packages/scDataLoader/meta.yaml | 3 ++ packages/scFates/meta.yaml | 2 ++ packages/scGen/meta.yaml | 2 ++ packages/scPRINT-2/meta.yaml | 4 +++ packages/scPRINT/meta.yaml | 4 +++ packages/scXpand/meta.yaml | 2 ++ packages/scanpro/meta.yaml | 2 ++ packages/scanpy/meta.yaml | 5 +++ packages/schist/meta.yaml | 2 ++ packages/scib-rapids/meta.yaml | 2 ++ packages/scib/meta.yaml | 2 ++ packages/scirpy/meta.yaml | 2 ++ packages/scmcp/meta.yaml | 2 ++ packages/sctriangulate/meta.yaml | 2 ++ packages/scvelo/meta.yaml | 2 ++ packages/scverse-tutorials/meta.yaml | 2 ++ packages/scverse.github.io/meta.yaml | 2 ++ packages/scvi-tools/meta.yaml | 4 +++ packages/scxmatch/meta.yaml | 3 ++ packages/scyan/meta.yaml | 4 +++ packages/sift-sc/meta.yaml | 2 ++ packages/sincei/meta.yaml | 4 +++ packages/sobolev-alignment/meta.yaml | 2 ++ packages/sopa/meta.yaml | 3 ++ packages/spatial-eggplant/meta.yaml | 3 ++ packages/spatialdata/meta.yaml | 3 ++ packages/spatialproteomics/meta.yaml | 4 +++ packages/spatiomic/meta.yaml | 5 +++ packages/squidpy/meta.yaml | 4 +++ packages/stats/meta.yaml | 2 ++ packages/symphonypy/meta.yaml | 3 ++ packages/tangram/meta.yaml | 3 ++ packages/tau-community-detection/meta.yaml | 2 ++ packages/vitessce/meta.yaml | 4 +++ packages/wsidata/meta.yaml | 3 ++ packages/zellkonverter/meta.yaml | 2 ++ scripts/src/ecosystem_scripts/schema.json | 31 ++++++++++++++++++ 120 files changed, 386 insertions(+) diff --git a/README.md b/README.md index 8c3ca50d..ef70d479 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,42 @@ Submit a pull-request adding a `meta.yaml` file for your package to the `package - Please refer to other entries for examples - The full definition of available fields is available in [`schema.json`](scripts/src/ecosystem_scripts/schema.json) - You can add a logo in svg/png/webp format if you like. Currently it is not used on our website, though. +- Please set `topics` from the controlled vocabulary below, in addition to free-form `tags` + +## Topics and tags + +Packages carry two kinds of keywords, and they do different jobs. + +`topics` say what a package is **for**. They come from a controlled vocabulary, are validated +against [`schema.json`](scripts/src/ecosystem_scripts/schema.json), and drive the filters on +[scverse.org/packages](https://scverse.org/packages/#ecosystem). Pick every topic that genuinely +applies, usually one to three. If none of them fit your package, propose a new one in your pull +request rather than forcing a bad match. + +| Topic | For packages that … | +| ----------------------- | -------------------------------------------------------------------------- | +| `annotation` | assign cell type or state labels, or transfer them from a reference | +| `cell-communication` | infer ligand–receptor interactions and cell–cell signalling | +| `clustering` | group cells, spots or genes into populations or domains | +| `deconvolution` | estimate cell type composition of mixed or bulk measurements | +| `differential-analysis` | test for differential expression or abundance, or score gene sets | +| `epigenomics` | work with chromatin accessibility, methylation or related modalities | +| `gene-networks` | infer regulatory networks, co-expression or gene programs | +| `imaging` | work with histology, microscopy or whole-slide images | +| `immune` | analyse immune receptor repertoires or are otherwise immunology-specific | +| `infrastructure` | provide data structures, file formats, I/O or tooling rather than analysis | +| `integration` | correct batch effects, map to references, or join datasets and modalities | +| `multi-omics` | jointly analyse two or more molecular modalities | +| `perturbation` | analyse CRISPR screens, drug response or other perturbation experiments | +| `preprocessing` | do quality control, filtering, normalisation or denoising | +| `proteomics` | work with mass spectrometry, cytometry or other protein measurements | +| `spatial` | work with spatially resolved measurements | +| `trajectory` | infer pseudotime, RNA velocity, lineage or cell fate | +| `visualization` | provide plotting, interactive exploration or data browsers | + +`tags` stay free-form and are only used for search, so they do not need to match anyone else's +spelling. Use them for anything the topics are too coarse to express — an assay, a method, a +platform, a dependency. ## What are the requirements for an ecosystem package? @@ -46,6 +82,7 @@ How does the package use scverse data structures (please describe in a few sente - [ ] Continuous integration (CI) automatically executes these tests on each push or pull request [^2] - [ ] The package provides API documentation via a website or README[^3] - [ ] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions) +- [ ] The `topics` field is set from the controlled vocabulary documented above - [ ] I am an author or maintainer of the tool and agree on listing the package on the scverse website ### Recommended diff --git a/packages/AESTETIK/meta.yaml b/packages/AESTETIK/meta.yaml index 9d5b25eb..09b79fb9 100644 --- a/packages/AESTETIK/meta.yaml +++ b/packages/AESTETIK/meta.yaml @@ -21,6 +21,10 @@ tags: - computational-pathology - deep learning - pytorch +topics: + - spatial + - imaging + - multi-omics license: MIT version: v0.3.1 contact: diff --git a/packages/CellAnnotator/meta.yaml b/packages/CellAnnotator/meta.yaml index 2a627f18..ac772b6a 100644 --- a/packages/CellAnnotator/meta.yaml +++ b/packages/CellAnnotator/meta.yaml @@ -11,6 +11,8 @@ tags: - large language models - automatic annotation - cell state +topics: + - annotation license: MIT version: v0.1.3 contact: diff --git a/packages/CellCharter/meta.yaml b/packages/CellCharter/meta.yaml index f77a73bc..177967ed 100644 --- a/packages/CellCharter/meta.yaml +++ b/packages/CellCharter/meta.yaml @@ -13,6 +13,10 @@ tags: - spatial clustering - spatial domains - gaussian mixture model +topics: + - spatial + - multi-omics + - clustering license: BSD-3-Clause version: v0.3.1 contact: diff --git a/packages/CellMapper/meta.yaml b/packages/CellMapper/meta.yaml index 2a67bfdc..d5004f01 100644 --- a/packages/CellMapper/meta.yaml +++ b/packages/CellMapper/meta.yaml @@ -10,6 +10,9 @@ tags: - rapids - faiss - query-to-reference +topics: + - integration + - annotation license: MIT version: v0.1.2 contact: diff --git a/packages/CellOracle/meta.yaml b/packages/CellOracle/meta.yaml index 503f0277..4c372a7c 100644 --- a/packages/CellOracle/meta.yaml +++ b/packages/CellOracle/meta.yaml @@ -12,6 +12,10 @@ install: tags: - GRN - TF +topics: + - gene-networks + - epigenomics + - perturbation license: Apache-2.0 version: v0.10.12 contact: diff --git a/packages/CellRank/meta.yaml b/packages/CellRank/meta.yaml index 0b2f2661..ab07a3c0 100644 --- a/packages/CellRank/meta.yaml +++ b/packages/CellRank/meta.yaml @@ -15,6 +15,8 @@ tags: - cell-fate - rna-velocity - trajectory-generation +topics: + - trajectory license: BSD-3-Clause version: v1.5.1 contact: diff --git a/packages/Cell_BLAST/meta.yaml b/packages/Cell_BLAST/meta.yaml index d1b72f69..c5fc1f31 100644 --- a/packages/Cell_BLAST/meta.yaml +++ b/packages/Cell_BLAST/meta.yaml @@ -9,6 +9,8 @@ install: pypi: Cell-BLAST tags: - BLAST +topics: + - annotation license: MIT version: v0.3.8 contact: diff --git a/packages/CellphoneDB/meta.yaml b/packages/CellphoneDB/meta.yaml index f41781b4..d96565bd 100644 --- a/packages/CellphoneDB/meta.yaml +++ b/packages/CellphoneDB/meta.yaml @@ -18,6 +18,8 @@ tags: - single-cell - python - jupyter +topics: + - cell-communication license: MIT version: v5.0.0 contact: diff --git a/packages/Cirrocumulus/meta.yaml b/packages/Cirrocumulus/meta.yaml index c2102e13..593da779 100644 --- a/packages/Cirrocumulus/meta.yaml +++ b/packages/Cirrocumulus/meta.yaml @@ -10,6 +10,8 @@ install: pypi: cirrocumulus tags: - visualization +topics: + - visualization license: BSD-3-Clause version: v1.1.41 contact: diff --git a/packages/DOTools_py/meta.yaml b/packages/DOTools_py/meta.yaml index 3836aab6..c4f35e13 100644 --- a/packages/DOTools_py/meta.yaml +++ b/packages/DOTools_py/meta.yaml @@ -10,6 +10,8 @@ tags: - python - visualisation - analysis +topics: + - visualization license: MIT version: v0.0.2 contact: diff --git a/packages/DRVI/meta.yaml b/packages/DRVI/meta.yaml index f2700ee6..b1bc8599 100644 --- a/packages/DRVI/meta.yaml +++ b/packages/DRVI/meta.yaml @@ -18,6 +18,8 @@ tags: - data integration - variational inference - deep learning +topics: + - integration license: BSD-3-Clause version: 0.2.0 contact: diff --git a/packages/DoubletDetection/meta.yaml b/packages/DoubletDetection/meta.yaml index 6cc2fd0d..a0636a8d 100644 --- a/packages/DoubletDetection/meta.yaml +++ b/packages/DoubletDetection/meta.yaml @@ -11,6 +11,8 @@ install: pypi: doubletdetection tags: - doublet +topics: + - preprocessing license: MIT version: v4.2 contact: diff --git a/packages/GPTBioInsightor/meta.yaml b/packages/GPTBioInsightor/meta.yaml index 8bd6f75e..4b38466a 100644 --- a/packages/GPTBioInsightor/meta.yaml +++ b/packages/GPTBioInsightor/meta.yaml @@ -11,6 +11,8 @@ tags: - bioinformatics - LLM - AI +topics: + - annotation license: BSD-3-Clause version: v0.3.0 contact: diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index 69164181..2d31fcf3 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -14,6 +14,9 @@ tags: - gene networks - format - utilities +topics: + - gene-networks + - infrastructure license: MIT version: v1.1.4 contact: diff --git a/packages/LazySlide/meta.yaml b/packages/LazySlide/meta.yaml index 98dc00d6..bad66e27 100644 --- a/packages/LazySlide/meta.yaml +++ b/packages/LazySlide/meta.yaml @@ -9,6 +9,9 @@ tags: - Pathology - Whole Slide Imaging - PyTorch +topics: + - imaging + - preprocessing license: MIT version: v0.3.0 contact: diff --git a/packages/Mowgli/meta.yaml b/packages/Mowgli/meta.yaml index 1009d028..df0e56ed 100644 --- a/packages/Mowgli/meta.yaml +++ b/packages/Mowgli/meta.yaml @@ -13,6 +13,9 @@ tags: - multi omics - data integration - NMF +topics: + - multi-omics + - integration license: GPL-3.0-only version: v0.2.0 contact: diff --git a/packages/Multivelo/meta.yaml b/packages/Multivelo/meta.yaml index 9b696232..d018dd5f 100644 --- a/packages/Multivelo/meta.yaml +++ b/packages/Multivelo/meta.yaml @@ -11,6 +11,9 @@ install: pypi: multivelo tags: - rna velocity +topics: + - trajectory + - epigenomics license: BSD-3-Clause version: 0.1.3 contact: diff --git a/packages/PEAKQC/meta.yaml b/packages/PEAKQC/meta.yaml index 3d3603bd..e7a0ed26 100644 --- a/packages/PEAKQC/meta.yaml +++ b/packages/PEAKQC/meta.yaml @@ -10,6 +10,9 @@ tags: - single cell - ATAC-seq - quality control +topics: + - epigenomics + - preprocessing license: MIT version: 0.1.3 contact: diff --git a/packages/PILOT/meta.yaml b/packages/PILOT/meta.yaml index eb6715f4..90a3bdc8 100644 --- a/packages/PILOT/meta.yaml +++ b/packages/PILOT/meta.yaml @@ -22,6 +22,9 @@ tags: - pathomics-data - ot - patient-level +topics: + - trajectory + - multi-omics license: MIT version: v2.0.6 contact: diff --git a/packages/ParTIpy/meta.yaml b/packages/ParTIpy/meta.yaml index 2c34ab2a..54a2a9aa 100644 --- a/packages/ParTIpy/meta.yaml +++ b/packages/ParTIpy/meta.yaml @@ -12,6 +12,9 @@ tags: - "archetypal analysis" - "division of labor" - "representation learning" +topics: + - clustering + - spatial version: v0.0.04 contact: - psl-schaefer diff --git a/packages/PathML/meta.yaml b/packages/PathML/meta.yaml index dcd97c21..0dc77c17 100644 --- a/packages/PathML/meta.yaml +++ b/packages/PathML/meta.yaml @@ -10,6 +10,8 @@ install: pypi: pathml tags: - pathology +topics: + - imaging license: GPL-2.0-only version: v2.1.0 contact: diff --git a/packages/PyDESeq2/meta.yaml b/packages/PyDESeq2/meta.yaml index f1af4d44..783e957e 100644 --- a/packages/PyDESeq2/meta.yaml +++ b/packages/PyDESeq2/meta.yaml @@ -11,6 +11,8 @@ license: MIT tags: - rna-seq - differential-expression +topics: + - differential-analysis publications: - 10.1101/2022.12.14.520412 version: v0.3.0 diff --git a/packages/Rectangle/meta.yaml b/packages/Rectangle/meta.yaml index b6b6a1bc..bd29ea01 100644 --- a/packages/Rectangle/meta.yaml +++ b/packages/Rectangle/meta.yaml @@ -11,6 +11,8 @@ license: MIT tags: - rna-seq - deconvolution +topics: + - deconvolution version: v0.1.6 contact: - bernheder diff --git a/packages/SC2Spa/meta.yaml b/packages/SC2Spa/meta.yaml index 53687c5e..aca039bb 100644 --- a/packages/SC2Spa/meta.yaml +++ b/packages/SC2Spa/meta.yaml @@ -15,6 +15,9 @@ tags: - spatial transcriptomics - deep learning - cell communication +topics: + - spatial + - integration license: BSD-3-Clause version: v1.2 contact: diff --git a/packages/SCALEX/meta.yaml b/packages/SCALEX/meta.yaml index d86c8662..48423d50 100644 --- a/packages/SCALEX/meta.yaml +++ b/packages/SCALEX/meta.yaml @@ -12,6 +12,9 @@ tags: - integration - projection - scATAC-seq +topics: + - integration + - epigenomics license: MIT version: v1.0.3 contact: diff --git a/packages/STMiner/meta.yaml b/packages/STMiner/meta.yaml index 531fdad1..0a0a63ad 100644 --- a/packages/STMiner/meta.yaml +++ b/packages/STMiner/meta.yaml @@ -10,6 +10,8 @@ tags: - spatial patterns - optimal transport - mechine learning +topics: + - spatial license: GPL-3.0-or-later version: v1.1.0 contact: diff --git a/packages/SnapATAC2/meta.yaml b/packages/SnapATAC2/meta.yaml index b39c0e8a..5a452744 100644 --- a/packages/SnapATAC2/meta.yaml +++ b/packages/SnapATAC2/meta.yaml @@ -15,6 +15,10 @@ tags: - ATAC-seq - chromatin accessibility - epigenomics +topics: + - epigenomics + - preprocessing + - clustering license: MIT version: 2.5.0 contact: diff --git a/packages/TreeData/meta.yaml b/packages/TreeData/meta.yaml index f0f26392..dd1edaf6 100644 --- a/packages/TreeData/meta.yaml +++ b/packages/TreeData/meta.yaml @@ -9,6 +9,9 @@ install: pypi: treedata tags: - lineage-tracing +topics: + - infrastructure + - trajectory license: BSD-3-Clause version: v0.2.2 contact: diff --git a/packages/alphapepttools/meta.yaml b/packages/alphapepttools/meta.yaml index 803497b6..e8f3626b 100644 --- a/packages/alphapepttools/meta.yaml +++ b/packages/alphapepttools/meta.yaml @@ -14,6 +14,9 @@ tags: - proteomics - annotated data - best practices +topics: + - proteomics + - infrastructure license: Apache-2.0 version: 0.2.0 contact: diff --git a/packages/anndata-for-R/meta.yaml b/packages/anndata-for-R/meta.yaml index cfceb042..564cef1b 100644 --- a/packages/anndata-for-R/meta.yaml +++ b/packages/anndata-for-R/meta.yaml @@ -14,6 +14,8 @@ tags: - data structures - interoperability - R +topics: + - infrastructure license: MIT version: 0.7.5.5 contact: diff --git a/packages/anndata/meta.yaml b/packages/anndata/meta.yaml index 578f75d9..7ed289f2 100644 --- a/packages/anndata/meta.yaml +++ b/packages/anndata/meta.yaml @@ -15,6 +15,8 @@ tags: - data structure - annotated data - sparse data +topics: + - infrastructure license: BSD-3-Clause version: 0.12.4 contact: diff --git a/packages/anndataR/meta.yaml b/packages/anndataR/meta.yaml index 30915432..1140e910 100644 --- a/packages/anndataR/meta.yaml +++ b/packages/anndataR/meta.yaml @@ -13,6 +13,8 @@ tags: - interoperability - R - Bioconductor +topics: + - infrastructure publications: - 10.1101/2025.08.18.669052 # bioRxiv preprint version: 1.0.0 diff --git a/packages/annsel/meta.yaml b/packages/annsel/meta.yaml index 6201ceea..43d83c8f 100644 --- a/packages/annsel/meta.yaml +++ b/packages/annsel/meta.yaml @@ -16,6 +16,8 @@ tags: - dataframe - accessor - utilities +topics: + - infrastructure test_command: | pip install ".[test]" && pytest category: ecosystem diff --git a/packages/benGRN/meta.yaml b/packages/benGRN/meta.yaml index dc768cb1..9c677dc4 100644 --- a/packages/benGRN/meta.yaml +++ b/packages/benGRN/meta.yaml @@ -13,6 +13,8 @@ tags: - RNAseq - gene network inference - benchmark +topics: + - gene-networks license: MIT version: v1.2.1 contact: diff --git a/packages/bento-tools/meta.yaml b/packages/bento-tools/meta.yaml index 86840863..ecb4feb1 100644 --- a/packages/bento-tools/meta.yaml +++ b/packages/bento-tools/meta.yaml @@ -10,6 +10,8 @@ install: pypi: bento-tools tags: - spatial analysis +topics: + - spatial license: BSD-2-Clause version: v1.0.1 contact: diff --git a/packages/biolord/meta.yaml b/packages/biolord/meta.yaml index 390bd05d..14738c82 100644 --- a/packages/biolord/meta.yaml +++ b/packages/biolord/meta.yaml @@ -10,6 +10,9 @@ tags: - single-cell - disentanglement - generative framework +topics: + - perturbation + - integration license: BSD-3-Clause version: v0.0.1 contact: diff --git a/packages/cell2location/meta.yaml b/packages/cell2location/meta.yaml index 83c1c0b2..738875c4 100644 --- a/packages/cell2location/meta.yaml +++ b/packages/cell2location/meta.yaml @@ -13,6 +13,9 @@ install: pypi: cell2location tags: - Bayesian +topics: + - spatial + - deconvolution license: Apache-2.0 version: v0.1 contact: diff --git a/packages/cellxgene/meta.yaml b/packages/cellxgene/meta.yaml index b3900017..33c5f9db 100644 --- a/packages/cellxgene/meta.yaml +++ b/packages/cellxgene/meta.yaml @@ -10,6 +10,9 @@ install: pypi: cellxgene tags: - HCA +topics: + - visualization + - annotation license: MIT version: 1.1.1 contact: diff --git a/packages/clone2vec/meta.yaml b/packages/clone2vec/meta.yaml index 82425f38..cc56d79a 100644 --- a/packages/clone2vec/meta.yaml +++ b/packages/clone2vec/meta.yaml @@ -8,6 +8,8 @@ install: pypi: clone2vec tags: - label-transfer +topics: + - trajectory license: MIT publications: - 10.1101/2024.11.15.623687 diff --git a/packages/cookiecutter-scverse/meta.yaml b/packages/cookiecutter-scverse/meta.yaml index 1324b53a..1eb44814 100644 --- a/packages/cookiecutter-scverse/meta.yaml +++ b/packages/cookiecutter-scverse/meta.yaml @@ -6,6 +6,8 @@ documentation_home: https://cookiecutter-scverse-instance.readthedocs.io/page/te tags: - template - cookiecutter +topics: + - infrastructure license: BSD-3-Clause version: 0.6.0 contact: diff --git a/packages/dandelion/meta.yaml b/packages/dandelion/meta.yaml index 81b41860..3e14cdce 100644 --- a/packages/dandelion/meta.yaml +++ b/packages/dandelion/meta.yaml @@ -16,6 +16,9 @@ tags: - dandelion - bcr - tcr +topics: + - immune + - preprocessing license: AGPL-3.0-or-later version: v0.3.0 contact: diff --git a/packages/decoupler/meta.yaml b/packages/decoupler/meta.yaml index a32a87a9..f7a564ac 100644 --- a/packages/decoupler/meta.yaml +++ b/packages/decoupler/meta.yaml @@ -15,6 +15,8 @@ tags: - pathway analysis - gene sets - functional annotation +topics: + - differential-analysis license: BSD-3-Clause version: 2.1.1 contact: diff --git a/packages/delnx/meta.yaml b/packages/delnx/meta.yaml index 0dd91937..cad53e1d 100644 --- a/packages/delnx/meta.yaml +++ b/packages/delnx/meta.yaml @@ -11,6 +11,8 @@ tags: - regression models - dispersion estimation - JAX +topics: + - differential-analysis license: MIT version: v0.2.3 contact: diff --git a/packages/dvp-io/meta.yaml b/packages/dvp-io/meta.yaml index 55cae01e..746e8e76 100644 --- a/packages/dvp-io/meta.yaml +++ b/packages/dvp-io/meta.yaml @@ -10,6 +10,10 @@ tags: - LC/MS-proteomics - Spatial Proteomics - Reader +topics: + - spatial + - proteomics + - infrastructure license: Apache-2.0 version: 0.5.1 contact: diff --git a/packages/dynamo-release/meta.yaml b/packages/dynamo-release/meta.yaml index 47a9111c..a76e6660 100644 --- a/packages/dynamo-release/meta.yaml +++ b/packages/dynamo-release/meta.yaml @@ -12,6 +12,9 @@ install: pypi: dynamo-release tags: - vector +topics: + - trajectory + - multi-omics license: BSD-3-Clause version: v1.1.0 contact: diff --git a/packages/ecosystem-packages/meta.yaml b/packages/ecosystem-packages/meta.yaml index 84b3c4af..1897fefd 100644 --- a/packages/ecosystem-packages/meta.yaml +++ b/packages/ecosystem-packages/meta.yaml @@ -6,6 +6,8 @@ documentation_home: https://github.com/scverse/ecosystem-packages tags: - registry - ecosystem +topics: + - infrastructure license: BSD-3-Clause contact: - grst diff --git a/packages/epiScanpy/meta.yaml b/packages/epiScanpy/meta.yaml index 64dbc5f2..e1b37238 100644 --- a/packages/epiScanpy/meta.yaml +++ b/packages/epiScanpy/meta.yaml @@ -12,6 +12,8 @@ install: tags: - scanpy - epigenomics +topics: + - epigenomics license: BSD-3-Clause version: v0.3.2 contact: diff --git a/packages/eschr/meta.yaml b/packages/eschr/meta.yaml index 6ba0bb5a..b4e97f2b 100644 --- a/packages/eschr/meta.yaml +++ b/packages/eschr/meta.yaml @@ -13,6 +13,8 @@ tags: - clustering - uncertainty - ensemble +topics: + - clustering license: "MIT" version: v1.0.1 contact: diff --git a/packages/favapy/meta.yaml b/packages/favapy/meta.yaml index 56cbbf92..bbed5d79 100644 --- a/packages/favapy/meta.yaml +++ b/packages/favapy/meta.yaml @@ -14,6 +14,8 @@ tags: - coexpression networks - functional associations - variational autoencoders +topics: + - gene-networks license: MIT version: v0.3.9.4 contact: diff --git a/packages/flashdeconv/meta.yaml b/packages/flashdeconv/meta.yaml index 77cf36a7..812e6f2e 100644 --- a/packages/flashdeconv/meta.yaml +++ b/packages/flashdeconv/meta.yaml @@ -18,6 +18,9 @@ tags: - cell type - Visium HD - sketching +topics: + - spatial + - deconvolution license: BSD-3-Clause version: v0.1 contact: diff --git a/packages/flowsom/meta.yaml b/packages/flowsom/meta.yaml index f69f2d09..b29831cc 100644 --- a/packages/flowsom/meta.yaml +++ b/packages/flowsom/meta.yaml @@ -17,6 +17,10 @@ install: tags: - clustering - flowcytometry +topics: + - proteomics + - clustering + - visualization license: GPL-3.0-only version: v0.0.1 contact: diff --git a/packages/governance/meta.yaml b/packages/governance/meta.yaml index f67f96a3..36fd8714 100644 --- a/packages/governance/meta.yaml +++ b/packages/governance/meta.yaml @@ -6,6 +6,8 @@ documentation_home: https://scverse.org/about tags: - governance - documentation +topics: + - infrastructure license: BSD-3-Clause contact: - Zethson diff --git a/packages/grassp/meta.yaml b/packages/grassp/meta.yaml index 4a20da5d..714072b0 100644 --- a/packages/grassp/meta.yaml +++ b/packages/grassp/meta.yaml @@ -13,6 +13,9 @@ tags: - subcellular proteomics - mass-spectrometry - graph-based analysis +topics: + - proteomics + - spatial license: BSD-3-Clause version: v0.1.0 contact: diff --git a/packages/gssnng/meta.yaml b/packages/gssnng/meta.yaml index 6d41f6f7..40264e06 100644 --- a/packages/gssnng/meta.yaml +++ b/packages/gssnng/meta.yaml @@ -14,6 +14,8 @@ tags: - geneset-scoring - smoothing - python +topics: + - differential-analysis license: MIT version: v0.4.2 contact: diff --git a/packages/hotspot/meta.yaml b/packages/hotspot/meta.yaml index 0ec6c1a9..ec69539f 100644 --- a/packages/hotspot/meta.yaml +++ b/packages/hotspot/meta.yaml @@ -10,6 +10,8 @@ install: pypi: hotspotsc tags: - gene-signatures +topics: + - gene-networks license: BSD-3-Clause version: v1.1.1 contact: diff --git a/packages/illico/meta.yaml b/packages/illico/meta.yaml index 7b6472c4..2c0b6fcc 100644 --- a/packages/illico/meta.yaml +++ b/packages/illico/meta.yaml @@ -10,6 +10,8 @@ install: tags: - differential-gene-expression - single-cell-RNA-seq +topics: + - differential-analysis license: Apache-2.0 version: 0.1.1 contact: diff --git a/packages/infercnvpy/meta.yaml b/packages/infercnvpy/meta.yaml index b97d1f5e..9aa129a8 100644 --- a/packages/infercnvpy/meta.yaml +++ b/packages/infercnvpy/meta.yaml @@ -8,6 +8,8 @@ install: pypi: infercnvpy tags: - CNV +topics: + - annotation license: BSD-3-Clause version: v0.3.0 contact: diff --git a/packages/integration-testing/meta.yaml b/packages/integration-testing/meta.yaml index 4e4a49b3..022bf3d1 100644 --- a/packages/integration-testing/meta.yaml +++ b/packages/integration-testing/meta.yaml @@ -6,6 +6,8 @@ documentation_home: https://github.com/scverse/integration-testing tags: - testing - continuous integration +topics: + - infrastructure license: MIT contact: - ilan-gold diff --git a/packages/kompot/meta.yaml b/packages/kompot/meta.yaml index e52c0beb..0ba5fa19 100644 --- a/packages/kompot/meta.yaml +++ b/packages/kompot/meta.yaml @@ -23,6 +23,8 @@ tags: - continuous representation - jax - anndata +topics: + - differential-analysis license: GPL-3.0-or-later version: v0.6.1 contact: diff --git a/packages/liana/meta.yaml b/packages/liana/meta.yaml index 11504563..6388e5b7 100644 --- a/packages/liana/meta.yaml +++ b/packages/liana/meta.yaml @@ -11,6 +11,9 @@ tags: - spatial - ligand-receptor - cell-cell communication +topics: + - cell-communication + - spatial license: GPL-3.0-only version: v1.0.0a1 contact: diff --git a/packages/maxspin/meta.yaml b/packages/maxspin/meta.yaml index 0e9944c9..2b380671 100644 --- a/packages/maxspin/meta.yaml +++ b/packages/maxspin/meta.yaml @@ -11,6 +11,9 @@ install: tags: - spatially varying genes - spatial autocorrelation +topics: + - spatial + - differential-analysis license: MIT version: v0.1.1 contact: diff --git a/packages/moscot/meta.yaml b/packages/moscot/meta.yaml index 5ccb5a1d..3443c8b1 100644 --- a/packages/moscot/meta.yaml +++ b/packages/moscot/meta.yaml @@ -12,6 +12,10 @@ tags: - trajectory inference - multi omics - spatial +topics: + - multi-omics + - trajectory + - spatial license: BSD-3-Clause version: v0.4.0 contact: diff --git a/packages/mudata/meta.yaml b/packages/mudata/meta.yaml index a5436a4c..a7063bb4 100644 --- a/packages/mudata/meta.yaml +++ b/packages/mudata/meta.yaml @@ -15,6 +15,9 @@ tags: - data structure - multimodal - multi-omics +topics: + - multi-omics + - infrastructure license: BSD-3-Clause version: 0.3.2 contact: diff --git a/packages/muon/meta.yaml b/packages/muon/meta.yaml index a9b3ddc9..4a9f9720 100644 --- a/packages/muon/meta.yaml +++ b/packages/muon/meta.yaml @@ -14,6 +14,10 @@ tags: - multimodal - multi-omics - integration +topics: + - multi-omics + - integration + - preprocessing license: BSD-3-Clause version: 0.1.7 contact: diff --git a/packages/nichepca/meta.yaml b/packages/nichepca/meta.yaml index 3b58ce20..9a40f34b 100644 --- a/packages/nichepca/meta.yaml +++ b/packages/nichepca/meta.yaml @@ -10,6 +10,9 @@ tags: - spatial-omics - spatial domain identification - spatial clustering +topics: + - spatial + - clustering license: MIT version: v0.0.3 contact: diff --git a/packages/novae/meta.yaml b/packages/novae/meta.yaml index 792c6371..8526ce90 100644 --- a/packages/novae/meta.yaml +++ b/packages/novae/meta.yaml @@ -13,6 +13,10 @@ tags: - spatial-transcriptomics - spatialdata - deep learning +topics: + - spatial + - clustering + - integration license: BSD-3-Clause version: v0.2.1 contact: diff --git a/packages/omicverse/meta.yaml b/packages/omicverse/meta.yaml index 92db0dba..6d1ef78f 100644 --- a/packages/omicverse/meta.yaml +++ b/packages/omicverse/meta.yaml @@ -14,6 +14,8 @@ tags: - bulk-rna-seq - omics - bioinformatics +topics: + - multi-omics license: GPL-3.0-only version: v1.4.12 contact: diff --git a/packages/palantir/meta.yaml b/packages/palantir/meta.yaml index 417bffc0..34541d5d 100644 --- a/packages/palantir/meta.yaml +++ b/packages/palantir/meta.yaml @@ -24,6 +24,8 @@ tags: - single-cell-genomics - cell-fate-transitions - scrna-seq-analysis +topics: + - trajectory license: GPL-2.0-or-later version: v1.3.3 contact: diff --git a/packages/panpipes/meta.yaml b/packages/panpipes/meta.yaml index 8cda09a2..81674a74 100644 --- a/packages/panpipes/meta.yaml +++ b/packages/panpipes/meta.yaml @@ -14,6 +14,9 @@ tags: - pipeline - spatial - bioinformatics +topics: + - multi-omics + - spatial license: BSD-3-Clause version: v0.5.0 contact: diff --git a/packages/pcdl/meta.yaml b/packages/pcdl/meta.yaml index cfdd8267..f52ba9e7 100644 --- a/packages/pcdl/meta.yaml +++ b/packages/pcdl/meta.yaml @@ -14,6 +14,8 @@ tags: - agent-based modeling - diffusion transport solver - newtonian physics +topics: + - infrastructure #publications: version: v4.0.4 category: ecosystem diff --git a/packages/pegasus/meta.yaml b/packages/pegasus/meta.yaml index 1f9f676a..4a23fdbf 100644 --- a/packages/pegasus/meta.yaml +++ b/packages/pegasus/meta.yaml @@ -10,6 +10,10 @@ install: pypi: pegasuspy tags: - transcriptome analysis +topics: + - preprocessing + - clustering + - annotation license: BSD-3-Clause version: v1.7.1 contact: diff --git a/packages/pertpy/meta.yaml b/packages/pertpy/meta.yaml index 33f0e9f2..8fc092f2 100644 --- a/packages/pertpy/meta.yaml +++ b/packages/pertpy/meta.yaml @@ -16,6 +16,9 @@ tags: - drug response - CRISPR - genetic perturbation +topics: + - perturbation + - differential-analysis license: MIT version: 1.0.3 contact: diff --git a/packages/popV/meta.yaml b/packages/popV/meta.yaml index 8ff69ec9..ee897a2b 100644 --- a/packages/popV/meta.yaml +++ b/packages/popV/meta.yaml @@ -9,6 +9,9 @@ tags: - cell type labels - batch integration - automatic annotation +topics: + - annotation + - integration license: MIT version: v0.5.2 contact: diff --git a/packages/pyCrossTalkeR/meta.yaml b/packages/pyCrossTalkeR/meta.yaml index a08f4cc1..7e923f13 100644 --- a/packages/pyCrossTalkeR/meta.yaml +++ b/packages/pyCrossTalkeR/meta.yaml @@ -10,6 +10,9 @@ tags: - CCI - scRNAseq - Node Importance +topics: + - cell-communication + - visualization license: MIT version: v2.1.0 contact: diff --git a/packages/pyLemur/meta.yaml b/packages/pyLemur/meta.yaml index 6053cf09..f13e967e 100644 --- a/packages/pyLemur/meta.yaml +++ b/packages/pyLemur/meta.yaml @@ -12,6 +12,8 @@ tags: - single-cell - differential expression - multi-condition +topics: + - differential-analysis license: MIT version: v0.1.0 contact: diff --git a/packages/pySCENIC/meta.yaml b/packages/pySCENIC/meta.yaml index d03c644b..a3dd8c2e 100644 --- a/packages/pySCENIC/meta.yaml +++ b/packages/pySCENIC/meta.yaml @@ -16,6 +16,9 @@ install: tags: - regulatory networks - clustering +topics: + - gene-networks + - clustering license: GPL-3.0-only version: v0.12.0 contact: diff --git a/packages/pyUCell/meta.yaml b/packages/pyUCell/meta.yaml index 943b27d3..7c461a6a 100644 --- a/packages/pyUCell/meta.yaml +++ b/packages/pyUCell/meta.yaml @@ -17,6 +17,8 @@ tags: - single-cell - signature scoring - module scoring +topics: + - differential-analysis license: MIT version: v0.3.0 contact: diff --git a/packages/pycea/meta.yaml b/packages/pycea/meta.yaml index 5b633cfc..a0b58c5c 100644 --- a/packages/pycea/meta.yaml +++ b/packages/pycea/meta.yaml @@ -9,6 +9,9 @@ install: tags: - lineage-tracing - TreeData +topics: + - trajectory + - visualization license: BSD-3-Clause version: v0.1.0 contact: diff --git a/packages/pychromVAR/meta.yaml b/packages/pychromVAR/meta.yaml index eaefa9b8..21c36e47 100644 --- a/packages/pychromVAR/meta.yaml +++ b/packages/pychromVAR/meta.yaml @@ -9,6 +9,8 @@ install: tags: - TF - scATAC-seq +topics: + - epigenomics license: MIT version: v0.0.3 contact: diff --git a/packages/pytximport/meta.yaml b/packages/pytximport/meta.yaml index 2d48fc45..2074ad87 100644 --- a/packages/pytximport/meta.yaml +++ b/packages/pytximport/meta.yaml @@ -10,6 +10,8 @@ tags: - rna-seq - bulk-rna-seq - differential-expression +topics: + - infrastructure license: GPL-3.0-only version: v0.2.0 contact: diff --git a/packages/rapids-singlecell/meta.yaml b/packages/rapids-singlecell/meta.yaml index c95c1bf2..ee4cefdc 100644 --- a/packages/rapids-singlecell/meta.yaml +++ b/packages/rapids-singlecell/meta.yaml @@ -12,6 +12,9 @@ tags: - single-cell - RAPIDS - CUDA +topics: + - preprocessing + - clustering license: MIT version: 0.13.3 contact: diff --git a/packages/scCellFie/meta.yaml b/packages/scCellFie/meta.yaml index f49538bd..1a4c7303 100644 --- a/packages/scCellFie/meta.yaml +++ b/packages/scCellFie/meta.yaml @@ -12,6 +12,10 @@ tags: - metabolism - metabolic activities - cell-cell communication +topics: + - differential-analysis + - spatial + - cell-communication license: MIT version: v0.4.5 contact: diff --git a/packages/scDataLoader/meta.yaml b/packages/scDataLoader/meta.yaml index bb77545f..ef034351 100644 --- a/packages/scDataLoader/meta.yaml +++ b/packages/scDataLoader/meta.yaml @@ -17,6 +17,9 @@ tags: - lightning - cellxgene - preprocessing +topics: + - infrastructure + - preprocessing license: MIT version: v1.2.2 contact: diff --git a/packages/scFates/meta.yaml b/packages/scFates/meta.yaml index 68923196..a6494ec5 100644 --- a/packages/scFates/meta.yaml +++ b/packages/scFates/meta.yaml @@ -12,6 +12,8 @@ tags: - pseudotime - cell-fate - trajectory-generation +topics: + - trajectory license: BSD-3-Clause version: v1.0.0 contact: diff --git a/packages/scGen/meta.yaml b/packages/scGen/meta.yaml index a15f822d..8f6db694 100644 --- a/packages/scGen/meta.yaml +++ b/packages/scGen/meta.yaml @@ -11,6 +11,8 @@ install: pypi: scgen tags: - perturbation +topics: + - perturbation license: GPL-3.0-only version: v2.1.0 contact: diff --git a/packages/scPRINT-2/meta.yaml b/packages/scPRINT-2/meta.yaml index 7033538d..3d7791ef 100644 --- a/packages/scPRINT-2/meta.yaml +++ b/packages/scPRINT-2/meta.yaml @@ -22,6 +22,10 @@ tags: - species integration - expression imputation - counterfactual predictions +topics: + - gene-networks + - annotation + - preprocessing license: GPL-3.0-or-later version: v1.0.0 contact: diff --git a/packages/scPRINT/meta.yaml b/packages/scPRINT/meta.yaml index ab50d3bf..60091de1 100644 --- a/packages/scPRINT/meta.yaml +++ b/packages/scPRINT/meta.yaml @@ -19,6 +19,10 @@ tags: - embedding - pytorch - lightning +topics: + - gene-networks + - annotation + - preprocessing license: MIT version: v1.6.2 contact: diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml index d8b41c6a..b310e69a 100644 --- a/packages/scXpand/meta.yaml +++ b/packages/scXpand/meta.yaml @@ -15,6 +15,8 @@ tags: - scTCR-seq - T-cell clonal expansion - machine learning +topics: + - immune license: MIT version: v0.4.3 contact: diff --git a/packages/scanpro/meta.yaml b/packages/scanpro/meta.yaml index 76ef198c..266a9dc3 100644 --- a/packages/scanpro/meta.yaml +++ b/packages/scanpro/meta.yaml @@ -11,6 +11,8 @@ tags: - single cell - proportion analysis - multi omics +topics: + - differential-analysis license: MIT version: 0.2.0 contact: diff --git a/packages/scanpy/meta.yaml b/packages/scanpy/meta.yaml index c799c640..c7722b91 100644 --- a/packages/scanpy/meta.yaml +++ b/packages/scanpy/meta.yaml @@ -18,6 +18,11 @@ tags: - clustering - visualization - differential expression +topics: + - preprocessing + - clustering + - differential-analysis + - visualization license: BSD-3-Clause version: 1.11.5 contact: diff --git a/packages/schist/meta.yaml b/packages/schist/meta.yaml index 5fde688f..3f430d8c 100644 --- a/packages/schist/meta.yaml +++ b/packages/schist/meta.yaml @@ -9,6 +9,8 @@ license: BSD-3-Clause tags: - clustering - single-cell +topics: + - clustering publications: - 10.1186/s12859-021-04489-7 version: v0.8.1 diff --git a/packages/scib-rapids/meta.yaml b/packages/scib-rapids/meta.yaml index cd2e2349..40b50748 100644 --- a/packages/scib-rapids/meta.yaml +++ b/packages/scib-rapids/meta.yaml @@ -12,6 +12,8 @@ tags: - data integration - GPU acceleration - RAPIDS +topics: + - integration license: BSD-3-Clause version: 0.1.0 contact: diff --git a/packages/scib/meta.yaml b/packages/scib/meta.yaml index 17f91009..7ad2514b 100644 --- a/packages/scib/meta.yaml +++ b/packages/scib/meta.yaml @@ -11,6 +11,8 @@ tags: - benchmarking - single cell - data integration +topics: + - integration license: MIT version: v1.0.5 contact: diff --git a/packages/scirpy/meta.yaml b/packages/scirpy/meta.yaml index 1c1b0dc2..7e88404b 100644 --- a/packages/scirpy/meta.yaml +++ b/packages/scirpy/meta.yaml @@ -16,6 +16,8 @@ tags: - TCR - BCR - AIRR +topics: + - immune license: BSD-3-Clause version: 0.22.3 contact: diff --git a/packages/scmcp/meta.yaml b/packages/scmcp/meta.yaml index a4e5dfdc..1ded0ef3 100644 --- a/packages/scmcp/meta.yaml +++ b/packages/scmcp/meta.yaml @@ -9,6 +9,8 @@ tags: - bioinformatics - LLM - AI +topics: + - infrastructure license: BSD-3-Clause version: v0.2.2 contact: diff --git a/packages/sctriangulate/meta.yaml b/packages/sctriangulate/meta.yaml index 5b31e45e..983e079a 100644 --- a/packages/sctriangulate/meta.yaml +++ b/packages/sctriangulate/meta.yaml @@ -10,6 +10,8 @@ install: pypi: sctriangulate tags: - clustering +topics: + - clustering license: MIT version: v0.12.0 contact: diff --git a/packages/scvelo/meta.yaml b/packages/scvelo/meta.yaml index 94344866..2063278b 100644 --- a/packages/scvelo/meta.yaml +++ b/packages/scvelo/meta.yaml @@ -9,6 +9,8 @@ install: pypi: scvelo tags: - rna velocity +topics: + - trajectory license: BSD-3-Clause version: v0.2.5 contact: diff --git a/packages/scverse-tutorials/meta.yaml b/packages/scverse-tutorials/meta.yaml index 9e72106c..3b0cc1e9 100644 --- a/packages/scverse-tutorials/meta.yaml +++ b/packages/scverse-tutorials/meta.yaml @@ -8,6 +8,8 @@ tags: - tutorials - education - documentation +topics: + - infrastructure license: BSD-3-Clause contact: - grst diff --git a/packages/scverse.github.io/meta.yaml b/packages/scverse.github.io/meta.yaml index 82bfc433..a27d8a0c 100644 --- a/packages/scverse.github.io/meta.yaml +++ b/packages/scverse.github.io/meta.yaml @@ -6,6 +6,8 @@ documentation_home: https://scverse.org tags: - website - documentation +topics: + - infrastructure license: BSD-3-Clause authors: - gtca diff --git a/packages/scvi-tools/meta.yaml b/packages/scvi-tools/meta.yaml index f96dbe9a..23ecd4c0 100644 --- a/packages/scvi-tools/meta.yaml +++ b/packages/scvi-tools/meta.yaml @@ -34,6 +34,10 @@ tags: - probabilistic models - variational inference - deep learning +topics: + - integration + - annotation + - differential-analysis license: BSD-3-Clause version: 1.4.0.post1 contact: diff --git a/packages/scxmatch/meta.yaml b/packages/scxmatch/meta.yaml index c599ad2b..ccca5753 100644 --- a/packages/scxmatch/meta.yaml +++ b/packages/scxmatch/meta.yaml @@ -17,6 +17,9 @@ tags: - distance-based matching - perturbation - condition +topics: + - perturbation + - differential-analysis license: MIT version: v0.1.0 contact: diff --git a/packages/scyan/meta.yaml b/packages/scyan/meta.yaml index fe33bc23..b9b5afe7 100644 --- a/packages/scyan/meta.yaml +++ b/packages/scyan/meta.yaml @@ -15,6 +15,10 @@ tags: - annotation - batch-effect correction - debarcoding +topics: + - proteomics + - annotation + - integration license: BSD-3-Clause version: v1.5.0 contact: diff --git a/packages/sift-sc/meta.yaml b/packages/sift-sc/meta.yaml index 6be22aac..41d092e8 100644 --- a/packages/sift-sc/meta.yaml +++ b/packages/sift-sc/meta.yaml @@ -11,6 +11,8 @@ tags: - single-cell - signals - filter +topics: + - preprocessing license: BSD-3-Clause version: v0.1.0 contact: diff --git a/packages/sincei/meta.yaml b/packages/sincei/meta.yaml index cf562e29..3f0dccad 100644 --- a/packages/sincei/meta.yaml +++ b/packages/sincei/meta.yaml @@ -20,6 +20,10 @@ tags: - epigenomics - multi omics - BAM +topics: + - epigenomics + - preprocessing + - clustering license: MIT version: v0.5.1 authors: diff --git a/packages/sobolev-alignment/meta.yaml b/packages/sobolev-alignment/meta.yaml index 83055ce1..4c3bbe1d 100644 --- a/packages/sobolev-alignment/meta.yaml +++ b/packages/sobolev-alignment/meta.yaml @@ -14,6 +14,8 @@ tags: - pre-clinical - clinical - scrnaseq +topics: + - integration license: MIT version: 1.0.0 contact: diff --git a/packages/sopa/meta.yaml b/packages/sopa/meta.yaml index 212dcc82..5b4beeee 100644 --- a/packages/sopa/meta.yaml +++ b/packages/sopa/meta.yaml @@ -15,6 +15,9 @@ tags: - multiplex imaging - spatialdata - pipeline +topics: + - spatial + - imaging license: BSD-3-Clause version: v1.0.0 contact: diff --git a/packages/spatial-eggplant/meta.yaml b/packages/spatial-eggplant/meta.yaml index 26cd1cb0..37982f57 100644 --- a/packages/spatial-eggplant/meta.yaml +++ b/packages/spatial-eggplant/meta.yaml @@ -11,6 +11,9 @@ install: tags: - spatial alignment - spatial registration +topics: + - spatial + - integration license: MIT version: v0.2.3 contact: diff --git a/packages/spatialdata/meta.yaml b/packages/spatialdata/meta.yaml index b1f6e126..b91effe9 100644 --- a/packages/spatialdata/meta.yaml +++ b/packages/spatialdata/meta.yaml @@ -14,6 +14,9 @@ tags: - data structure - spatial omics - FAIR +topics: + - spatial + - infrastructure license: BSD-3-Clause version: 0.5.0 contact: diff --git a/packages/spatialproteomics/meta.yaml b/packages/spatialproteomics/meta.yaml index 855ca35b..6d6cdd9c 100644 --- a/packages/spatialproteomics/meta.yaml +++ b/packages/spatialproteomics/meta.yaml @@ -14,6 +14,10 @@ tags: - multiplex imaging - spatialdata - pipeline +topics: + - spatial + - proteomics + - imaging license: MIT version: v0.7.0 contact: diff --git a/packages/spatiomic/meta.yaml b/packages/spatiomic/meta.yaml index 809938b2..e1083d37 100644 --- a/packages/spatiomic/meta.yaml +++ b/packages/spatiomic/meta.yaml @@ -13,6 +13,11 @@ tags: - multiplexed protein imaging - PathoPlex - subcellular analysis +topics: + - spatial + - proteomics + - imaging + - clustering license: GPL-3.0-only version: v0.5.0 contact: diff --git a/packages/squidpy/meta.yaml b/packages/squidpy/meta.yaml index 2f525b81..b3a11e2c 100644 --- a/packages/squidpy/meta.yaml +++ b/packages/squidpy/meta.yaml @@ -16,6 +16,10 @@ tags: - spatial omics - spatial transcriptomics - image analysis +topics: + - spatial + - imaging + - visualization license: BSD-3-Clause version: 1.6.5 contact: diff --git a/packages/stats/meta.yaml b/packages/stats/meta.yaml index 61cd2eb8..0f215e40 100644 --- a/packages/stats/meta.yaml +++ b/packages/stats/meta.yaml @@ -6,6 +6,8 @@ documentation_home: https://scverse.org/stats/ tags: - statistics - metrics +topics: + - infrastructure license: MIT authors: - maltekuehl diff --git a/packages/symphonypy/meta.yaml b/packages/symphonypy/meta.yaml index 9734db0b..c4f1f7d5 100644 --- a/packages/symphonypy/meta.yaml +++ b/packages/symphonypy/meta.yaml @@ -8,6 +8,9 @@ install: pypi: symphonypy tags: - label-transfer +topics: + - annotation + - integration license: GPL-3.0-only version: v0.2.1 contact: diff --git a/packages/tangram/meta.yaml b/packages/tangram/meta.yaml index 9081c8ce..f2dd70b6 100644 --- a/packages/tangram/meta.yaml +++ b/packages/tangram/meta.yaml @@ -11,6 +11,9 @@ install: tags: - spatial decomposition - spatial mapping +topics: + - spatial + - integration license: BSD-3-Clause version: v1.0.3 contact: diff --git a/packages/tau-community-detection/meta.yaml b/packages/tau-community-detection/meta.yaml index 58ed87e0..050469aa 100644 --- a/packages/tau-community-detection/meta.yaml +++ b/packages/tau-community-detection/meta.yaml @@ -16,6 +16,8 @@ tags: - scanpy - anndata - graph-analysis +topics: + - clustering publications: - 10.1093/pnasnexus/pgad180 version: 1.4.7 diff --git a/packages/vitessce/meta.yaml b/packages/vitessce/meta.yaml index 9d3573a0..00812f8d 100644 --- a/packages/vitessce/meta.yaml +++ b/packages/vitessce/meta.yaml @@ -11,6 +11,10 @@ install: pypi: vitessce tags: - imaging +topics: + - visualization + - spatial + - imaging license: MIT version: v3.5.7 contact: diff --git a/packages/wsidata/meta.yaml b/packages/wsidata/meta.yaml index bee8e6f8..8932877b 100644 --- a/packages/wsidata/meta.yaml +++ b/packages/wsidata/meta.yaml @@ -8,6 +8,9 @@ install: tags: - Pathology - Whole Slide Imaging +topics: + - imaging + - infrastructure license: MIT version: v0.3.0 contact: diff --git a/packages/zellkonverter/meta.yaml b/packages/zellkonverter/meta.yaml index 653082e5..6161e467 100644 --- a/packages/zellkonverter/meta.yaml +++ b/packages/zellkonverter/meta.yaml @@ -14,6 +14,8 @@ tags: - interoperability - R - Bioconductor +topics: + - infrastructure version: 1.20.0 contact: - lazappi diff --git a/scripts/src/ecosystem_scripts/schema.json b/scripts/src/ecosystem_scripts/schema.json index d753063b..02643a73 100644 --- a/scripts/src/ecosystem_scripts/schema.json +++ b/scripts/src/ecosystem_scripts/schema.json @@ -195,6 +195,36 @@ "minItems": 1, "uniqueItems": true }, + "topics": { + "description": "What the package is for, from a controlled vocabulary. Drives the filters on scverse.org/packages. Pick every topic that genuinely applies, usually one to three. Propose additions in a pull request.", + "type": "array", + "items": { + "type": "string", + "enum": [ + "annotation", + "cell-communication", + "clustering", + "deconvolution", + "differential-analysis", + "epigenomics", + "gene-networks", + "imaging", + "immune", + "infrastructure", + "integration", + "multi-omics", + "perturbation", + "preprocessing", + "proteomics", + "spatial", + "trajectory", + "visualization" + ] + }, + "minItems": 1, + "maxItems": 4, + "uniqueItems": true + }, "publications": { "description": "DOIs of publications describing the package", "type": "array", @@ -244,6 +274,7 @@ "documentation_home", "license", "tags", + "topics", "category" ], "if": { From e68bdc2c7019233724e09c828bd24eb9349cdf18 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Tue, 11 Aug 2026 13:47:22 +0200 Subject: [PATCH 2/6] One sentence per line in the README prose --- README.md | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index ef70d479..19432d4e 100644 --- a/README.md +++ b/README.md @@ -26,11 +26,10 @@ Submit a pull-request adding a `meta.yaml` file for your package to the `package Packages carry two kinds of keywords, and they do different jobs. -`topics` say what a package is **for**. They come from a controlled vocabulary, are validated -against [`schema.json`](scripts/src/ecosystem_scripts/schema.json), and drive the filters on -[scverse.org/packages](https://scverse.org/packages/#ecosystem). Pick every topic that genuinely -applies, usually one to three. If none of them fit your package, propose a new one in your pull -request rather than forcing a bad match. +`topics` say what a package is **for**. +They come from a controlled vocabulary, are validated against [`schema.json`](scripts/src/ecosystem_scripts/schema.json), and drive the filters on [scverse.org/packages](https://scverse.org/packages/#ecosystem). +Pick every topic that genuinely applies, usually one to three. +If none of them fit your package, propose a new one in your pull request rather than forcing a bad match. | Topic | For packages that … | | ----------------------- | -------------------------------------------------------------------------- | @@ -53,9 +52,8 @@ request rather than forcing a bad match. | `trajectory` | infer pseudotime, RNA velocity, lineage or cell fate | | `visualization` | provide plotting, interactive exploration or data browsers | -`tags` stay free-form and are only used for search, so they do not need to match anyone else's -spelling. Use them for anything the topics are too coarse to express — an assay, a method, a -platform, a dependency. +`tags` stay free-form and are only used for search, so they do not need to match anyone else's spelling. +Use them for anything the topics are too coarse to express — an assay, a method, a platform, a dependency. ## What are the requirements for an ecosystem package? From dbc9e0091e20199ffa2774f04726af9cc40919eb Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Thu, 13 Aug 2026 10:16:46 +0200 Subject: [PATCH 3/6] Replace free-form tags with a controlled vocabulary, category and language Follows the review: no free-form tags at all, and the vocabulary is collapsed out of the tags that already existed rather than invented. `tags` becomes a 45-term enum, folded from the 250 distinct tags in the registry, with the non-descriptive ones dropped (`python`, `single-cell`, `bioinformatics`, `utilities`, library names). `primary_category` names the one category a package is listed under. Both mirror the tutorial registry, which already solved this, so the two registries share terminology instead of inventing their own. `language` is assumed to be Python unless set, and marks the three R packages. Closes scverse/scverse.github.io#106, closes #299, closes #46. --- README.md | 73 +++++++++-------- packages/AESTETIK/meta.yaml | 14 +--- packages/CellAnnotator/meta.yaml | 8 +- packages/CellCharter/meta.yaml | 10 +-- packages/CellMapper/meta.yaml | 10 +-- packages/CellOracle/meta.yaml | 6 +- packages/CellRank/meta.yaml | 10 +-- packages/Cell_BLAST/meta.yaml | 6 +- packages/CellphoneDB/meta.yaml | 7 +- packages/Cirrocumulus/meta.yaml | 3 +- packages/DOTools_py/meta.yaml | 5 +- packages/DRVI/meta.yaml | 8 +- packages/DoubletDetection/meta.yaml | 5 +- packages/GPTBioInsightor/meta.yaml | 9 +-- packages/GRnnData/meta.yaml | 12 +-- packages/LazySlide/meta.yaml | 7 +- packages/Mowgli/meta.yaml | 11 +-- packages/Multivelo/meta.yaml | 5 +- packages/PEAKQC/meta.yaml | 5 +- packages/PILOT/meta.yaml | 14 ++-- packages/ParTIpy/meta.yaml | 9 +-- packages/PathML/meta.yaml | 3 +- packages/PyDESeq2/meta.yaml | 7 +- packages/Rectangle/meta.yaml | 5 +- packages/SC2Spa/meta.yaml | 7 +- packages/SCALEX/meta.yaml | 9 +-- packages/STMiner/meta.yaml | 9 +-- packages/SnapATAC2/meta.yaml | 6 +- packages/TreeData/meta.yaml | 7 +- packages/alphapepttools/meta.yaml | 7 +- packages/anndata-for-R/meta.yaml | 5 +- packages/anndata/meta.yaml | 7 +- packages/anndataR/meta.yaml | 6 +- packages/annsel/meta.yaml | 8 +- packages/benGRN/meta.yaml | 10 +-- packages/bento-tools/meta.yaml | 6 +- packages/biolord/meta.yaml | 8 +- packages/cell2location/meta.yaml | 7 +- packages/cellxgene/meta.yaml | 5 +- packages/clone2vec/meta.yaml | 5 +- packages/cookiecutter-scverse/meta.yaml | 6 +- packages/dandelion/meta.yaml | 8 +- packages/decoupler/meta.yaml | 8 +- packages/delnx/meta.yaml | 6 +- packages/dvp-io/meta.yaml | 9 +-- packages/dynamo-release/meta.yaml | 8 +- packages/ecosystem-packages/meta.yaml | 6 +- packages/epiScanpy/meta.yaml | 4 +- packages/eschr/meta.yaml | 6 +- packages/favapy/meta.yaml | 9 +-- packages/flashdeconv/meta.yaml | 8 +- packages/flowsom/meta.yaml | 7 +- packages/governance/meta.yaml | 4 +- packages/grassp/meta.yaml | 7 +- packages/gssnng/meta.yaml | 9 +-- packages/hotspot/meta.yaml | 6 +- packages/illico/meta.yaml | 7 +- packages/infercnvpy/meta.yaml | 5 +- packages/integration-testing/meta.yaml | 6 +- packages/kompot/meta.yaml | 14 +--- packages/liana/meta.yaml | 8 +- packages/maxspin/meta.yaml | 7 +- packages/moscot/meta.yaml | 11 +-- packages/mudata/meta.yaml | 7 +- packages/muon/meta.yaml | 8 +- packages/nichepca/meta.yaml | 7 +- packages/novae/meta.yaml | 9 +-- packages/omicverse/meta.yaml | 9 +-- packages/palantir/meta.yaml | 16 +--- packages/panpipes/meta.yaml | 10 +-- packages/pcdl/meta.yaml | 11 +-- packages/pegasus/meta.yaml | 6 +- packages/pertpy/meta.yaml | 8 +- packages/popV/meta.yaml | 9 +-- packages/pyCrossTalkeR/meta.yaml | 9 +-- packages/pyLemur/meta.yaml | 5 +- packages/pySCENIC/meta.yaml | 6 +- packages/pyUCell/meta.yaml | 7 +- packages/pycea/meta.yaml | 8 +- packages/pychromVAR/meta.yaml | 7 +- packages/pytximport/meta.yaml | 9 +-- packages/rapids-singlecell/meta.yaml | 7 +- packages/scCellFie/meta.yaml | 11 +-- packages/scDataLoader/meta.yaml | 13 +-- packages/scFates/meta.yaml | 6 +- packages/scGen/meta.yaml | 3 +- packages/scPRINT-2/meta.yaml | 26 +++--- packages/scPRINT/meta.yaml | 21 ++--- packages/scXpand/meta.yaml | 9 +-- packages/scanpro/meta.yaml | 8 +- packages/scanpy/meta.yaml | 7 +- packages/schist/meta.yaml | 4 +- packages/scib-rapids/meta.yaml | 7 +- packages/scib/meta.yaml | 6 +- packages/scirpy/meta.yaml | 6 +- packages/scmcp/meta.yaml | 8 +- packages/sctriangulate/meta.yaml | 3 +- packages/scvelo/meta.yaml | 5 +- packages/scverse-tutorials/meta.yaml | 5 +- packages/scverse.github.io/meta.yaml | 4 +- packages/scvi-tools/meta.yaml | 12 ++- packages/scxmatch/meta.yaml | 10 +-- packages/scyan/meta.yaml | 12 +-- packages/sift-sc/meta.yaml | 5 +- packages/sincei/meta.yaml | 12 +-- packages/sobolev-alignment/meta.yaml | 12 +-- packages/sopa/meta.yaml | 10 +-- packages/spatial-eggplant/meta.yaml | 8 +- packages/spatialdata/meta.yaml | 10 +-- packages/spatialproteomics/meta.yaml | 12 +-- packages/spatiomic/meta.yaml | 12 +-- packages/squidpy/meta.yaml | 6 +- packages/stats/meta.yaml | 6 +- packages/symphonypy/meta.yaml | 6 +- packages/tangram/meta.yaml | 8 +- packages/tau-community-detection/meta.yaml | 8 +- packages/vitessce/meta.yaml | 6 +- packages/wsidata/meta.yaml | 7 +- packages/zellkonverter/meta.yaml | 6 +- scripts/src/ecosystem_scripts/schema.json | 94 +++++++++++++++------- 120 files changed, 408 insertions(+), 697 deletions(-) diff --git a/README.md b/README.md index 19432d4e..cc8c3d9e 100644 --- a/README.md +++ b/README.md @@ -20,40 +20,40 @@ Submit a pull-request adding a `meta.yaml` file for your package to the `package - Please refer to other entries for examples - The full definition of available fields is available in [`schema.json`](scripts/src/ecosystem_scripts/schema.json) - You can add a logo in svg/png/webp format if you like. Currently it is not used on our website, though. -- Please set `topics` from the controlled vocabulary below, in addition to free-form `tags` - -## Topics and tags - -Packages carry two kinds of keywords, and they do different jobs. - -`topics` say what a package is **for**. -They come from a controlled vocabulary, are validated against [`schema.json`](scripts/src/ecosystem_scripts/schema.json), and drive the filters on [scverse.org/packages](https://scverse.org/packages/#ecosystem). -Pick every topic that genuinely applies, usually one to three. -If none of them fit your package, propose a new one in your pull request rather than forcing a bad match. - -| Topic | For packages that … | -| ----------------------- | -------------------------------------------------------------------------- | -| `annotation` | assign cell type or state labels, or transfer them from a reference | -| `cell-communication` | infer ligand–receptor interactions and cell–cell signalling | -| `clustering` | group cells, spots or genes into populations or domains | -| `deconvolution` | estimate cell type composition of mixed or bulk measurements | -| `differential-analysis` | test for differential expression or abundance, or score gene sets | -| `epigenomics` | work with chromatin accessibility, methylation or related modalities | -| `gene-networks` | infer regulatory networks, co-expression or gene programs | -| `imaging` | work with histology, microscopy or whole-slide images | -| `immune` | analyse immune receptor repertoires or are otherwise immunology-specific | -| `infrastructure` | provide data structures, file formats, I/O or tooling rather than analysis | -| `integration` | correct batch effects, map to references, or join datasets and modalities | -| `multi-omics` | jointly analyse two or more molecular modalities | -| `perturbation` | analyse CRISPR screens, drug response or other perturbation experiments | -| `preprocessing` | do quality control, filtering, normalisation or denoising | -| `proteomics` | work with mass spectrometry, cytometry or other protein measurements | -| `spatial` | work with spatially resolved measurements | -| `trajectory` | infer pseudotime, RNA velocity, lineage or cell fate | -| `visualization` | provide plotting, interactive exploration or data browsers | - -`tags` stay free-form and are only used for search, so they do not need to match anyone else's spelling. -Use them for anything the topics are too coarse to express — an assay, a method, a platform, a dependency. +- Please set `primary_category` and `tags` from the controlled vocabulary below + +## Categories, tags and language + +Keywords are a controlled vocabulary rather than free text, so that the same concept is not spelled three different ways across the registry. +The vocabulary is defined in [`schema.json`](scripts/src/ecosystem_scripts/schema.json) and validated in CI, and it deliberately overlaps with the one used by the [tutorial registry](https://github.com/scverse/scverse-tutorials/blob/main/tutorial-registry/schema.json). + +`primary_category` is the single category your package is listed under on [scverse.org/packages](https://scverse.org/packages/#ecosystem). +Pick the one a user looking for your package would browse first. + +- `Data structures` +- `scRNA-seq` +- `bulk RNA-seq` +- `Spatial` +- `Epigenomics` +- `Proteomics` +- `Adaptive immune cell receptor` +- `Multimodal` +- `Imaging` +- `Infrastructure` + +`tags` say what the package does, and drive filtering and search on the website. +Pick every tag that genuinely applies. + +- **Data and modality** — `scRNA-seq`, `bulk RNA-seq`, `spatial transcriptomics`, `spatial proteomics`, `proteomics`, `flow cytometry`, `ATAC-seq`, `epigenomics`, `immune receptor`, `imaging`, `multimodal` +- **Analysis step** — `preprocessing`, `quality control`, `denoising`, `data integration`, `cell-type annotation`, `differential expression`, `compositional analysis`, `functional analysis`, `gene regulatory networks`, `cell-cell communication`, `deconvolution`, `clustering`, `dimensionality reduction`, `trajectory inference`, `pseudotime`, `RNA velocity`, `lineage tracing`, `perturbation`, `spatially variable genes`, `segmentation`, `copy number variation`, `visualization`, `benchmarking` +- **How it is built** — `deep learning`, `foundation model`, `large language models`, `probabilistic modeling`, `optimal transport`, `GPU acceleration`, `pipeline` +- **Project shape** — `data structures`, `interoperability`, `file formats`, `documentation` + +If none of the existing terms fit your package, add one to the enum in your pull request and say why. +That is a deliberate speed bump: it keeps the vocabulary small enough to be useful, while letting it grow when the science does. + +`language` is the language you write in when using the package. +It is assumed to be `Python` when omitted, so only set it if that is wrong. ## What are the requirements for an ecosystem package? @@ -61,6 +61,8 @@ For a package to become an approved ecosystem package, it must fulfill all manda Ecosystem packages can be written in non-Python languages as long as they fulfill the above requirements. +Authors of ecosystem packages agree to abide by the [scverse code of conduct](https://scverse.org/about/code_of_conduct/) on all scverse communication channels. + If you cannot or do not want to comply with these requirements, you are still free to make your package interoperable with scverse by using our datastructures, but we will not list your package on our ecosystem page. ## Checklist for adding packages @@ -80,8 +82,9 @@ How does the package use scverse data structures (please describe in a few sente - [ ] Continuous integration (CI) automatically executes these tests on each push or pull request [^2] - [ ] The package provides API documentation via a website or README[^3] - [ ] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions) -- [ ] The `topics` field is set from the controlled vocabulary documented above +- [ ] `primary_category` and `tags` are set from the controlled vocabulary documented above - [ ] I am an author or maintainer of the tool and agree on listing the package on the scverse website +- [ ] I agree to abide by the [scverse code of conduct](https://scverse.org/about/code_of_conduct/) on all scverse communication channels ### Recommended diff --git a/packages/AESTETIK/meta.yaml b/packages/AESTETIK/meta.yaml index 09b79fb9..44e806ea 100644 --- a/packages/AESTETIK/meta.yaml +++ b/packages/AESTETIK/meta.yaml @@ -12,19 +12,13 @@ publications: - 10.1101/2024.06.04.24308256 install: pypi: aestetik +primary_category: Spatial tags: - - spatial-omics - - spatial-transcriptomics - - representation-learning - - autoencoder + - spatial transcriptomics + - imaging - multimodal - - computational-pathology + - dimensionality reduction - deep learning - - pytorch -topics: - - spatial - - imaging - - multi-omics license: MIT version: v0.3.1 contact: diff --git a/packages/CellAnnotator/meta.yaml b/packages/CellAnnotator/meta.yaml index ac772b6a..f4263a05 100644 --- a/packages/CellAnnotator/meta.yaml +++ b/packages/CellAnnotator/meta.yaml @@ -5,14 +5,10 @@ project_home: https://github.com/quadbio/cell-annotator documentation_home: https://cell-annotator.readthedocs.io/ install: pypi: cell-annotator +primary_category: scRNA-seq tags: - - cell type labels - - openai + - cell-type annotation - large language models - - automatic annotation - - cell state -topics: - - annotation license: MIT version: v0.1.3 contact: diff --git a/packages/CellCharter/meta.yaml b/packages/CellCharter/meta.yaml index 177967ed..9f005ed4 100644 --- a/packages/CellCharter/meta.yaml +++ b/packages/CellCharter/meta.yaml @@ -8,15 +8,11 @@ publications: - 10.1038/s41588-023-01588-4 install: pypi: cellcharter +primary_category: Spatial tags: - - spatial omics - - spatial clustering - - spatial domains - - gaussian mixture model -topics: - - spatial - - multi-omics + - spatial transcriptomics - clustering + - probabilistic modeling license: BSD-3-Clause version: v0.3.1 contact: diff --git a/packages/CellMapper/meta.yaml b/packages/CellMapper/meta.yaml index d5004f01..be88c3bd 100644 --- a/packages/CellMapper/meta.yaml +++ b/packages/CellMapper/meta.yaml @@ -5,14 +5,10 @@ project_home: https://github.com/quadbio/cellmapper documentation_home: https://cellmapper.readthedocs.io/ install: pypi: cellmapper +primary_category: scRNA-seq tags: - - k-NN based mapping - - rapids - - faiss - - query-to-reference -topics: - - integration - - annotation + - data integration + - GPU acceleration license: MIT version: v0.1.2 contact: diff --git a/packages/CellOracle/meta.yaml b/packages/CellOracle/meta.yaml index 4c372a7c..caa9819e 100644 --- a/packages/CellOracle/meta.yaml +++ b/packages/CellOracle/meta.yaml @@ -9,12 +9,10 @@ publications: - 10.1101/2020.02.17.947416 install: pypi: celloracle +primary_category: Epigenomics tags: - - GRN - - TF -topics: - - gene-networks - epigenomics + - gene regulatory networks - perturbation license: Apache-2.0 version: v0.10.12 diff --git a/packages/CellRank/meta.yaml b/packages/CellRank/meta.yaml index ab07a3c0..4ec95486 100644 --- a/packages/CellRank/meta.yaml +++ b/packages/CellRank/meta.yaml @@ -10,13 +10,11 @@ publications: - 10.1038/s41592-021-01346-6 install: pypi: cellrank +primary_category: scRNA-seq tags: - - ML - - cell-fate - - rna-velocity - - trajectory-generation -topics: - - trajectory + - trajectory inference + - RNA velocity + - deep learning license: BSD-3-Clause version: v1.5.1 contact: diff --git a/packages/Cell_BLAST/meta.yaml b/packages/Cell_BLAST/meta.yaml index c5fc1f31..858ba1ce 100644 --- a/packages/Cell_BLAST/meta.yaml +++ b/packages/Cell_BLAST/meta.yaml @@ -7,10 +7,10 @@ publications: - 10.1038/s41467-020-17281-7 install: pypi: Cell-BLAST +primary_category: scRNA-seq tags: - - BLAST -topics: - - annotation + - data integration + - cell-type annotation license: MIT version: v0.3.8 contact: diff --git a/packages/CellphoneDB/meta.yaml b/packages/CellphoneDB/meta.yaml index d96565bd..54670f1c 100644 --- a/packages/CellphoneDB/meta.yaml +++ b/packages/CellphoneDB/meta.yaml @@ -11,15 +11,10 @@ publications: - 10.1038/s41586-022-04918-4 install: pypi: cellphonedb +primary_category: scRNA-seq tags: - scRNA-seq - cell-cell communication - - ligand-receptor - - single-cell - - python - - jupyter -topics: - - cell-communication license: MIT version: v5.0.0 contact: diff --git a/packages/Cirrocumulus/meta.yaml b/packages/Cirrocumulus/meta.yaml index 593da779..8ed16591 100644 --- a/packages/Cirrocumulus/meta.yaml +++ b/packages/Cirrocumulus/meta.yaml @@ -8,10 +8,9 @@ publications: - 10.1038/s41592-020-0905-x install: pypi: cirrocumulus +primary_category: scRNA-seq tags: - visualization -topics: - - visualization license: BSD-3-Clause version: v1.1.41 contact: diff --git a/packages/DOTools_py/meta.yaml b/packages/DOTools_py/meta.yaml index c4f35e13..7b9ff8fc 100644 --- a/packages/DOTools_py/meta.yaml +++ b/packages/DOTools_py/meta.yaml @@ -5,12 +5,9 @@ documentation_home: https://dotools-py.readthedocs.io/ tutorials_home: https://dotools-py.readthedocs.io/ install: pypi: DOtools-py +primary_category: scRNA-seq tags: - scRNA-seq - - python - - visualisation - - analysis -topics: - visualization license: MIT version: v0.0.2 diff --git a/packages/DRVI/meta.yaml b/packages/DRVI/meta.yaml index b1bc8599..41ff3a0c 100644 --- a/packages/DRVI/meta.yaml +++ b/packages/DRVI/meta.yaml @@ -12,14 +12,12 @@ publications: - 10.1101/2024.11.06.622266 install: pypi: drvi-py +primary_category: scRNA-seq tags: - - disentanglement - - interpretability - data integration - - variational inference + - dimensionality reduction - deep learning -topics: - - integration + - probabilistic modeling license: BSD-3-Clause version: 0.2.0 contact: diff --git a/packages/DoubletDetection/meta.yaml b/packages/DoubletDetection/meta.yaml index a0636a8d..602618b0 100644 --- a/packages/DoubletDetection/meta.yaml +++ b/packages/DoubletDetection/meta.yaml @@ -9,10 +9,9 @@ publications: - 10.1016/j.cels.2019.03.003 install: pypi: doubletdetection +primary_category: scRNA-seq tags: - - doublet -topics: - - preprocessing + - quality control license: MIT version: v4.2 contact: diff --git a/packages/GPTBioInsightor/meta.yaml b/packages/GPTBioInsightor/meta.yaml index 4b38466a..40a9e675 100644 --- a/packages/GPTBioInsightor/meta.yaml +++ b/packages/GPTBioInsightor/meta.yaml @@ -6,13 +6,10 @@ project_home: https://github.com/huang-sh/GPTBioInsightor documentation_home: https://gptbioinsightor.readthedocs.io/ install: pypi: gptbioinsightor +primary_category: scRNA-seq tags: - - single-cell - - bioinformatics - - LLM - - AI -topics: - - annotation + - deep learning + - large language models license: BSD-3-Clause version: v0.3.0 contact: diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index 2d31fcf3..36204a32 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -8,15 +8,11 @@ publications: - 10.1101/2024.07.29.605556 install: pypi: grnndata +primary_category: Data structures tags: - - single cell - - RNAseq - - gene networks - - format - - utilities -topics: - - gene-networks - - infrastructure + - scRNA-seq + - gene regulatory networks + - file formats license: MIT version: v1.1.4 contact: diff --git a/packages/LazySlide/meta.yaml b/packages/LazySlide/meta.yaml index bad66e27..35bd0db9 100644 --- a/packages/LazySlide/meta.yaml +++ b/packages/LazySlide/meta.yaml @@ -5,13 +5,12 @@ project_home: https://github.com/rendeirolab/lazyslide documentation_home: https://lazyslide.readthedocs.io/ install: pypi: lazyslide +primary_category: Imaging tags: - - Pathology - - Whole Slide Imaging - - PyTorch -topics: - imaging - preprocessing + - segmentation + - deep learning license: MIT version: v0.3.0 contact: diff --git a/packages/Mowgli/meta.yaml b/packages/Mowgli/meta.yaml index df0e56ed..54373a65 100644 --- a/packages/Mowgli/meta.yaml +++ b/packages/Mowgli/meta.yaml @@ -7,15 +7,12 @@ publications: - 10.1101/2023.02.02.526825 install: pypi: mowgli +primary_category: Multimodal tags: - - single cell - - optimal transport - - multi omics + - multimodal - data integration - - NMF -topics: - - multi-omics - - integration + - dimensionality reduction + - optimal transport license: GPL-3.0-only version: v0.2.0 contact: diff --git a/packages/Multivelo/meta.yaml b/packages/Multivelo/meta.yaml index d018dd5f..1206831a 100644 --- a/packages/Multivelo/meta.yaml +++ b/packages/Multivelo/meta.yaml @@ -9,11 +9,10 @@ publications: - 10.1038/s41587-022-01476-y install: pypi: multivelo +primary_category: Epigenomics tags: - - rna velocity -topics: - - trajectory - epigenomics + - RNA velocity license: BSD-3-Clause version: 0.1.3 contact: diff --git a/packages/PEAKQC/meta.yaml b/packages/PEAKQC/meta.yaml index e7a0ed26..0c903e6d 100644 --- a/packages/PEAKQC/meta.yaml +++ b/packages/PEAKQC/meta.yaml @@ -6,13 +6,10 @@ publications: - 10.1101/2025.02.20.639146 install: pypi: peakqc +primary_category: Epigenomics tags: - - single cell - ATAC-seq - quality control -topics: - - epigenomics - - preprocessing license: MIT version: 0.1.3 contact: diff --git a/packages/PILOT/meta.yaml b/packages/PILOT/meta.yaml index 90a3bdc8..d74b9bee 100644 --- a/packages/PILOT/meta.yaml +++ b/packages/PILOT/meta.yaml @@ -15,16 +15,12 @@ install: # Install the PILOT package from PyPI pip install pilotpy pypi: pilotpy +primary_category: Multimodal tags: - - multi-omics - - single-cell - - trajectory - - pathomics-data - - ot - - patient-level -topics: - - trajectory - - multi-omics + - imaging + - multimodal + - trajectory inference + - optimal transport license: MIT version: v2.0.6 contact: diff --git a/packages/ParTIpy/meta.yaml b/packages/ParTIpy/meta.yaml index 54a2a9aa..d0ee7097 100644 --- a/packages/ParTIpy/meta.yaml +++ b/packages/ParTIpy/meta.yaml @@ -7,14 +7,9 @@ tutorials_home: https://partipy.readthedocs.io/ install: pypi: partipy license: MIT +primary_category: scRNA-seq tags: - - "single cell" - - "archetypal analysis" - - "division of labor" - - "representation learning" -topics: - - clustering - - spatial + - dimensionality reduction version: v0.0.04 contact: - psl-schaefer diff --git a/packages/PathML/meta.yaml b/packages/PathML/meta.yaml index 0dc77c17..fccce163 100644 --- a/packages/PathML/meta.yaml +++ b/packages/PathML/meta.yaml @@ -8,9 +8,8 @@ publications: - 10.1158/1541-7786.MCR-21-0665 install: pypi: pathml +primary_category: Imaging tags: - - pathology -topics: - imaging license: GPL-2.0-only version: v2.1.0 diff --git a/packages/PyDESeq2/meta.yaml b/packages/PyDESeq2/meta.yaml index 783e957e..df28fcb3 100644 --- a/packages/PyDESeq2/meta.yaml +++ b/packages/PyDESeq2/meta.yaml @@ -8,11 +8,10 @@ tutorials_home: https://pydeseq2.readthedocs.io/page/auto_examples/ install: pypi: pydeseq2 license: MIT +primary_category: bulk RNA-seq tags: - - rna-seq - - differential-expression -topics: - - differential-analysis + - bulk RNA-seq + - differential expression publications: - 10.1101/2022.12.14.520412 version: v0.3.0 diff --git a/packages/Rectangle/meta.yaml b/packages/Rectangle/meta.yaml index bd29ea01..23b29c5b 100644 --- a/packages/Rectangle/meta.yaml +++ b/packages/Rectangle/meta.yaml @@ -8,10 +8,9 @@ tutorials_home: https://rectanglepy.readthedocs.io/notebooks/example.html install: pypi: rectanglepy license: MIT +primary_category: bulk RNA-seq tags: - - rna-seq - - deconvolution -topics: + - bulk RNA-seq - deconvolution version: v0.1.6 contact: diff --git a/packages/SC2Spa/meta.yaml b/packages/SC2Spa/meta.yaml index aca039bb..09da8f8d 100644 --- a/packages/SC2Spa/meta.yaml +++ b/packages/SC2Spa/meta.yaml @@ -9,15 +9,12 @@ project_home: https://github.com/linbuliao/SC2Spa documentation_home: https://sc2spa.readthedocs.io/ install: pypi: SC2Spa +primary_category: Spatial tags: - - spatial inference - scRNA-seq - spatial transcriptomics + - cell-cell communication - deep learning - - cell communication -topics: - - spatial - - integration license: BSD-3-Clause version: v1.2 contact: diff --git a/packages/SCALEX/meta.yaml b/packages/SCALEX/meta.yaml index 48423d50..49a62ecb 100644 --- a/packages/SCALEX/meta.yaml +++ b/packages/SCALEX/meta.yaml @@ -7,14 +7,11 @@ publications: - 10.1038/s41467-022-33758-z install: pypi: SCALEX +primary_category: Multimodal tags: - scRNA-seq - - integration - - projection - - scATAC-seq -topics: - - integration - - epigenomics + - ATAC-seq + - data integration license: MIT version: v1.0.3 contact: diff --git a/packages/STMiner/meta.yaml b/packages/STMiner/meta.yaml index 0a0a63ad..3cf65fba 100644 --- a/packages/STMiner/meta.yaml +++ b/packages/STMiner/meta.yaml @@ -5,13 +5,12 @@ project_home: https://github.com/xjtu-omics/STMiner documentation_home: https://stminerdoc.readthedocs.io/ install: pypi: stminer +primary_category: Spatial tags: - - spatial variable genes - - spatial patterns + - spatial transcriptomics + - spatially variable genes + - deep learning - optimal transport - - mechine learning -topics: - - spatial license: GPL-3.0-or-later version: v1.1.0 contact: diff --git a/packages/SnapATAC2/meta.yaml b/packages/SnapATAC2/meta.yaml index 5a452744..13d6a766 100644 --- a/packages/SnapATAC2/meta.yaml +++ b/packages/SnapATAC2/meta.yaml @@ -11,14 +11,10 @@ publications: install: pypi: snapatac2 conda: bioconda::snapatac2 +primary_category: Epigenomics tags: - ATAC-seq - - chromatin accessibility - epigenomics -topics: - - epigenomics - - preprocessing - - clustering license: MIT version: 2.5.0 contact: diff --git a/packages/TreeData/meta.yaml b/packages/TreeData/meta.yaml index dd1edaf6..305aaa49 100644 --- a/packages/TreeData/meta.yaml +++ b/packages/TreeData/meta.yaml @@ -7,11 +7,10 @@ documentation_home: https://treedata.readthedocs.io/ tutorials_home: https://treedata.readthedocs.io/ install: pypi: treedata +primary_category: Data structures tags: - - lineage-tracing -topics: - - infrastructure - - trajectory + - lineage tracing + - data structures license: BSD-3-Clause version: v0.2.2 contact: diff --git a/packages/alphapepttools/meta.yaml b/packages/alphapepttools/meta.yaml index e8f3626b..d8282ad1 100644 --- a/packages/alphapepttools/meta.yaml +++ b/packages/alphapepttools/meta.yaml @@ -10,13 +10,10 @@ documentation_home: https://mannlabs.github.io/alphapepttools/index.html tutorials_home: https://github.com/MannLabs/alphapepttools/tree/main/docs/notebooks install: pypi: alphapepttools +primary_category: Proteomics tags: - proteomics - - annotated data - - best practices -topics: - - proteomics - - infrastructure + - file formats license: Apache-2.0 version: 0.2.0 contact: diff --git a/packages/anndata-for-R/meta.yaml b/packages/anndata-for-R/meta.yaml index 564cef1b..a7f99dd7 100644 --- a/packages/anndata-for-R/meta.yaml +++ b/packages/anndata-for-R/meta.yaml @@ -10,13 +10,12 @@ project_home: https://github.com/dynverse/anndata documentation_home: https://anndata.dynverse.org install: cran: anndata +primary_category: Data structures tags: - data structures - interoperability - - R -topics: - - infrastructure license: MIT +language: R version: 0.7.5.5 contact: - rcannood diff --git a/packages/anndata/meta.yaml b/packages/anndata/meta.yaml index 7ed289f2..95dac8de 100644 --- a/packages/anndata/meta.yaml +++ b/packages/anndata/meta.yaml @@ -11,12 +11,9 @@ publications: install: pypi: anndata conda: conda-forge::anndata +primary_category: Data structures tags: - - data structure - - annotated data - - sparse data -topics: - - infrastructure + - data structures license: BSD-3-Clause version: 0.12.4 contact: diff --git a/packages/anndataR/meta.yaml b/packages/anndataR/meta.yaml index 1140e910..3a809121 100644 --- a/packages/anndataR/meta.yaml +++ b/packages/anndataR/meta.yaml @@ -8,13 +8,11 @@ tutorials_home: https://scverse.org/anndataR/ install: bioconductor: anndataR license: MIT +language: R +primary_category: Data structures tags: - data structures - interoperability - - R - - Bioconductor -topics: - - infrastructure publications: - 10.1101/2025.08.18.669052 # bioRxiv preprint version: 1.0.0 diff --git a/packages/annsel/meta.yaml b/packages/annsel/meta.yaml index 43d83c8f..6b3a3a00 100644 --- a/packages/annsel/meta.yaml +++ b/packages/annsel/meta.yaml @@ -11,13 +11,9 @@ license: MIT version: v0.0.8 contact: - srivarra +primary_category: Data structures tags: - - narwhals - - dataframe - - accessor - - utilities -topics: - - infrastructure + - data structures test_command: | pip install ".[test]" && pytest category: ecosystem diff --git a/packages/benGRN/meta.yaml b/packages/benGRN/meta.yaml index 9c677dc4..977204e1 100644 --- a/packages/benGRN/meta.yaml +++ b/packages/benGRN/meta.yaml @@ -8,13 +8,11 @@ publications: - 10.1101/2024.07.29.605556 install: pypi: bengrn +primary_category: scRNA-seq tags: - - single cell - - RNAseq - - gene network inference - - benchmark -topics: - - gene-networks + - scRNA-seq + - gene regulatory networks + - benchmarking license: MIT version: v1.2.1 contact: diff --git a/packages/bento-tools/meta.yaml b/packages/bento-tools/meta.yaml index ecb4feb1..baf6ac7b 100644 --- a/packages/bento-tools/meta.yaml +++ b/packages/bento-tools/meta.yaml @@ -8,10 +8,10 @@ publications: - 10.1101/2022.06.10.495510 install: pypi: bento-tools +primary_category: Spatial tags: - - spatial analysis -topics: - - spatial + - spatial transcriptomics + - segmentation license: BSD-2-Clause version: v1.0.1 contact: diff --git a/packages/biolord/meta.yaml b/packages/biolord/meta.yaml index 14738c82..07127a77 100644 --- a/packages/biolord/meta.yaml +++ b/packages/biolord/meta.yaml @@ -6,13 +6,11 @@ documentation_home: https://biolord.readthedocs.io/ tutorials_home: https://biolord.readthedocs.io/ install: pypi: biolord +primary_category: scRNA-seq tags: - - single-cell - - disentanglement - - generative framework -topics: + - dimensionality reduction - perturbation - - integration + - deep learning license: BSD-3-Clause version: v0.0.1 contact: diff --git a/packages/cell2location/meta.yaml b/packages/cell2location/meta.yaml index 738875c4..0207feec 100644 --- a/packages/cell2location/meta.yaml +++ b/packages/cell2location/meta.yaml @@ -11,11 +11,12 @@ publications: - 10.1038/s41587-021-01139-4 install: pypi: cell2location +primary_category: Spatial tags: - - Bayesian -topics: - - spatial + - spatial transcriptomics + - cell-type annotation - deconvolution + - probabilistic modeling license: Apache-2.0 version: v0.1 contact: diff --git a/packages/cellxgene/meta.yaml b/packages/cellxgene/meta.yaml index 33c5f9db..4b462aa3 100644 --- a/packages/cellxgene/meta.yaml +++ b/packages/cellxgene/meta.yaml @@ -8,11 +8,10 @@ publications: - 10.1101/2021.04.05.438318 install: pypi: cellxgene +primary_category: scRNA-seq tags: - - HCA -topics: + - cell-type annotation - visualization - - annotation license: MIT version: 1.1.1 contact: diff --git a/packages/clone2vec/meta.yaml b/packages/clone2vec/meta.yaml index cc56d79a..7d87ef79 100644 --- a/packages/clone2vec/meta.yaml +++ b/packages/clone2vec/meta.yaml @@ -6,10 +6,9 @@ documentation_home: https://clone2vec.readthedocs.io/ tutorials_home: https://clone2vec.readthedocs.io/ install: pypi: clone2vec +primary_category: scRNA-seq tags: - - label-transfer -topics: - - trajectory + - lineage tracing license: MIT publications: - 10.1101/2024.11.15.623687 diff --git a/packages/cookiecutter-scverse/meta.yaml b/packages/cookiecutter-scverse/meta.yaml index 1eb44814..c6f3f619 100644 --- a/packages/cookiecutter-scverse/meta.yaml +++ b/packages/cookiecutter-scverse/meta.yaml @@ -3,11 +3,9 @@ description: | Cookiecutter template for scverse packages offering automated template sync project_home: https://github.com/scverse/cookiecutter-scverse documentation_home: https://cookiecutter-scverse-instance.readthedocs.io/page/template_usage.html +primary_category: Infrastructure tags: - - template - - cookiecutter -topics: - - infrastructure + - documentation license: BSD-3-Clause version: 0.6.0 contact: diff --git a/packages/dandelion/meta.yaml b/packages/dandelion/meta.yaml index 3e14cdce..56f8ba6b 100644 --- a/packages/dandelion/meta.yaml +++ b/packages/dandelion/meta.yaml @@ -12,13 +12,9 @@ publications: - 10.1101/2022.11.18.517068 install: pypi: sc-dandelion +primary_category: Adaptive immune cell receptor tags: - - dandelion - - bcr - - tcr -topics: - - immune - - preprocessing + - immune receptor license: AGPL-3.0-or-later version: v0.3.0 contact: diff --git a/packages/decoupler/meta.yaml b/packages/decoupler/meta.yaml index f7a564ac..a43e0890 100644 --- a/packages/decoupler/meta.yaml +++ b/packages/decoupler/meta.yaml @@ -10,13 +10,9 @@ publications: install: pypi: decoupler conda: conda-forge::decoupler-py +primary_category: scRNA-seq tags: - - enrichment analysis - - pathway analysis - - gene sets - - functional annotation -topics: - - differential-analysis + - functional analysis license: BSD-3-Clause version: 2.1.1 contact: diff --git a/packages/delnx/meta.yaml b/packages/delnx/meta.yaml index cad53e1d..8d545768 100644 --- a/packages/delnx/meta.yaml +++ b/packages/delnx/meta.yaml @@ -6,13 +6,9 @@ documentation_home: https://delnx.readthedocs.io/ tutorials_home: https://delnx.readthedocs.io/ install: pypi: delnx +primary_category: scRNA-seq tags: - differential expression - - regression models - - dispersion estimation - - JAX -topics: - - differential-analysis license: MIT version: v0.2.3 contact: diff --git a/packages/dvp-io/meta.yaml b/packages/dvp-io/meta.yaml index 746e8e76..fa838436 100644 --- a/packages/dvp-io/meta.yaml +++ b/packages/dvp-io/meta.yaml @@ -6,14 +6,11 @@ documentation_home: https://dvp-io.readthedocs.io tutorials_home: https://dvp-io.readthedocs.io/page/tutorials.html install: pypi: dvp-io +primary_category: Spatial tags: - - LC/MS-proteomics - - Spatial Proteomics - - Reader -topics: - - spatial + - spatial proteomics - proteomics - - infrastructure + - file formats license: Apache-2.0 version: 0.5.1 contact: diff --git a/packages/dynamo-release/meta.yaml b/packages/dynamo-release/meta.yaml index a76e6660..50eb7042 100644 --- a/packages/dynamo-release/meta.yaml +++ b/packages/dynamo-release/meta.yaml @@ -10,11 +10,11 @@ publications: - 10.1016/j.cell.2021.12.045 install: pypi: dynamo-release +primary_category: Multimodal tags: - - vector -topics: - - trajectory - - multi-omics + - multimodal + - trajectory inference + - RNA velocity license: BSD-3-Clause version: v1.1.0 contact: diff --git a/packages/ecosystem-packages/meta.yaml b/packages/ecosystem-packages/meta.yaml index 1897fefd..56c3d4a1 100644 --- a/packages/ecosystem-packages/meta.yaml +++ b/packages/ecosystem-packages/meta.yaml @@ -3,11 +3,9 @@ description: | Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem) project_home: https://github.com/scverse/ecosystem-packages documentation_home: https://github.com/scverse/ecosystem-packages +primary_category: Infrastructure tags: - - registry - - ecosystem -topics: - - infrastructure + - documentation license: BSD-3-Clause contact: - grst diff --git a/packages/epiScanpy/meta.yaml b/packages/epiScanpy/meta.yaml index e1b37238..009e6b96 100644 --- a/packages/epiScanpy/meta.yaml +++ b/packages/epiScanpy/meta.yaml @@ -9,10 +9,8 @@ publications: - 10.1038/s41467-021-25131-3 install: pypi: episcanpy +primary_category: Epigenomics tags: - - scanpy - - epigenomics -topics: - epigenomics license: BSD-3-Clause version: v0.3.2 diff --git a/packages/eschr/meta.yaml b/packages/eschr/meta.yaml index b4e97f2b..1d6215e4 100644 --- a/packages/eschr/meta.yaml +++ b/packages/eschr/meta.yaml @@ -9,12 +9,10 @@ publications: - 10.1186/s13059-024-03386-5 install: pypi: eschr +primary_category: scRNA-seq tags: - clustering - - uncertainty - - ensemble -topics: - - clustering + - probabilistic modeling license: "MIT" version: v1.0.1 contact: diff --git a/packages/favapy/meta.yaml b/packages/favapy/meta.yaml index bbed5d79..a66ecddc 100644 --- a/packages/favapy/meta.yaml +++ b/packages/favapy/meta.yaml @@ -10,12 +10,11 @@ publications: - 10.1093/nar/gkac1000 install: pypi: favapy +primary_category: scRNA-seq tags: - - coexpression networks - - functional associations - - variational autoencoders -topics: - - gene-networks + - gene regulatory networks + - dimensionality reduction + - deep learning license: MIT version: v0.3.9.4 contact: diff --git a/packages/flashdeconv/meta.yaml b/packages/flashdeconv/meta.yaml index 812e6f2e..62d8476d 100644 --- a/packages/flashdeconv/meta.yaml +++ b/packages/flashdeconv/meta.yaml @@ -12,14 +12,10 @@ publications: - 10.64898/2025.12.22.696108 install: pypi: flashdeconv +primary_category: Spatial tags: - spatial transcriptomics - - deconvolution - - cell type - - Visium HD - - sketching -topics: - - spatial + - cell-type annotation - deconvolution license: BSD-3-Clause version: v0.1 diff --git a/packages/flowsom/meta.yaml b/packages/flowsom/meta.yaml index b29831cc..25f08647 100644 --- a/packages/flowsom/meta.yaml +++ b/packages/flowsom/meta.yaml @@ -14,13 +14,10 @@ publications: - 10.1038/s41596-021-00550-0 install: conda: conda-forge::flowsom +primary_category: Proteomics tags: + - flow cytometry - clustering - - flowcytometry -topics: - - proteomics - - clustering - - visualization license: GPL-3.0-only version: v0.0.1 contact: diff --git a/packages/governance/meta.yaml b/packages/governance/meta.yaml index 36fd8714..57dc3f56 100644 --- a/packages/governance/meta.yaml +++ b/packages/governance/meta.yaml @@ -3,11 +3,9 @@ description: | Governance docs for scverse project_home: https://github.com/scverse/governance documentation_home: https://scverse.org/about +primary_category: Infrastructure tags: - - governance - documentation -topics: - - infrastructure license: BSD-3-Clause contact: - Zethson diff --git a/packages/grassp/meta.yaml b/packages/grassp/meta.yaml index 714072b0..3e90db77 100644 --- a/packages/grassp/meta.yaml +++ b/packages/grassp/meta.yaml @@ -9,13 +9,10 @@ documentation_home: https://public.czbiohub.org/comp.bio/grassp/ tutorials_home: https://public.czbiohub.org/comp.bio/grassp/tutorials/ install: pypi: grassp +primary_category: Spatial tags: - - subcellular proteomics - - mass-spectrometry - - graph-based analysis -topics: + - spatial proteomics - proteomics - - spatial license: BSD-3-Clause version: v0.1.0 contact: diff --git a/packages/gssnng/meta.yaml b/packages/gssnng/meta.yaml index 40264e06..2e58e568 100644 --- a/packages/gssnng/meta.yaml +++ b/packages/gssnng/meta.yaml @@ -8,14 +8,11 @@ publications: - 10.1093/bioadv/vbad150 install: pypi: gssnng +primary_category: scRNA-seq tags: - scRNA-seq - - GSEA - - geneset-scoring - - smoothing - - python -topics: - - differential-analysis + - preprocessing + - functional analysis license: MIT version: v0.4.2 contact: diff --git a/packages/hotspot/meta.yaml b/packages/hotspot/meta.yaml index ec69539f..e0974c5b 100644 --- a/packages/hotspot/meta.yaml +++ b/packages/hotspot/meta.yaml @@ -8,10 +8,10 @@ publications: - 10.1016/j.cels.2021.04.005 install: pypi: hotspotsc +primary_category: scRNA-seq tags: - - gene-signatures -topics: - - gene-networks + - functional analysis + - gene regulatory networks license: BSD-3-Clause version: v1.1.1 contact: diff --git a/packages/illico/meta.yaml b/packages/illico/meta.yaml index 2c0b6fcc..844797d4 100644 --- a/packages/illico/meta.yaml +++ b/packages/illico/meta.yaml @@ -7,11 +7,10 @@ tutorials_home: https://github.com/remydubois/illico publications: [] install: pypi: illico +primary_category: scRNA-seq tags: - - differential-gene-expression - - single-cell-RNA-seq -topics: - - differential-analysis + - scRNA-seq + - differential expression license: Apache-2.0 version: 0.1.1 contact: diff --git a/packages/infercnvpy/meta.yaml b/packages/infercnvpy/meta.yaml index 9aa129a8..809eb0a6 100644 --- a/packages/infercnvpy/meta.yaml +++ b/packages/infercnvpy/meta.yaml @@ -6,10 +6,9 @@ documentation_home: https://infercnvpy.readthedocs.io/ tutorials_home: https://infercnvpy.readthedocs.io/page/tutorials.html install: pypi: infercnvpy +primary_category: scRNA-seq tags: - - CNV -topics: - - annotation + - copy number variation license: BSD-3-Clause version: v0.3.0 contact: diff --git a/packages/integration-testing/meta.yaml b/packages/integration-testing/meta.yaml index 022bf3d1..68f4b57c 100644 --- a/packages/integration-testing/meta.yaml +++ b/packages/integration-testing/meta.yaml @@ -3,11 +3,9 @@ description: | A repo for integration testing core packages against upstream core packages project_home: https://github.com/scverse/integration-testing documentation_home: https://github.com/scverse/integration-testing +primary_category: Infrastructure tags: - - testing - - continuous integration -topics: - - infrastructure + - benchmarking license: MIT contact: - ilan-gold diff --git a/packages/kompot/meta.yaml b/packages/kompot/meta.yaml index 0ba5fa19..a75ccd2c 100644 --- a/packages/kompot/meta.yaml +++ b/packages/kompot/meta.yaml @@ -14,17 +14,11 @@ publications: install: pypi: kompot conda: bioconda::kompot +primary_category: scRNA-seq tags: - - differential-expression - - differential-abundance - - mahalanobis-distance - - gaussian-process - - phenotypic manifold - - continuous representation - - jax - - anndata -topics: - - differential-analysis + - differential expression + - compositional analysis + - probabilistic modeling license: GPL-3.0-or-later version: v0.6.1 contact: diff --git a/packages/liana/meta.yaml b/packages/liana/meta.yaml index 6388e5b7..f9be4f50 100644 --- a/packages/liana/meta.yaml +++ b/packages/liana/meta.yaml @@ -6,14 +6,10 @@ documentation_home: https://liana-py.readthedocs.io/ tutorials_home: https://liana-py.readthedocs.io/ install: pypi: liana +primary_category: scRNA-seq tags: - - single-cell - - spatial - - ligand-receptor + - spatial transcriptomics - cell-cell communication -topics: - - cell-communication - - spatial license: GPL-3.0-only version: v1.0.0a1 contact: diff --git a/packages/maxspin/meta.yaml b/packages/maxspin/meta.yaml index 2b380671..973fc66d 100644 --- a/packages/maxspin/meta.yaml +++ b/packages/maxspin/meta.yaml @@ -8,12 +8,9 @@ documentation_home: https://maxspin.readthedocs.io/ tutorials_home: https://github.com/dcjones/maxspin/blob/main/tutorial.ipynb install: pypi: maxspin +primary_category: Spatial tags: - - spatially varying genes - - spatial autocorrelation -topics: - - spatial - - differential-analysis + - spatially variable genes license: MIT version: v0.1.1 contact: diff --git a/packages/moscot/meta.yaml b/packages/moscot/meta.yaml index 3443c8b1..8604b1c5 100644 --- a/packages/moscot/meta.yaml +++ b/packages/moscot/meta.yaml @@ -7,15 +7,12 @@ publications: - 10.1101/2023.05.11.540374 install: pypi: moscot +primary_category: Multimodal tags: - - optimal transport + - spatial transcriptomics + - multimodal - trajectory inference - - multi omics - - spatial -topics: - - multi-omics - - trajectory - - spatial + - optimal transport license: BSD-3-Clause version: v0.4.0 contact: diff --git a/packages/mudata/meta.yaml b/packages/mudata/meta.yaml index a7063bb4..eb58af5c 100644 --- a/packages/mudata/meta.yaml +++ b/packages/mudata/meta.yaml @@ -11,13 +11,10 @@ publications: install: pypi: mudata conda: conda-forge::mudata +primary_category: Data structures tags: - - data structure - multimodal - - multi-omics -topics: - - multi-omics - - infrastructure + - data structures license: BSD-3-Clause version: 0.3.2 contact: diff --git a/packages/muon/meta.yaml b/packages/muon/meta.yaml index 4a9f9720..63f890e2 100644 --- a/packages/muon/meta.yaml +++ b/packages/muon/meta.yaml @@ -10,14 +10,10 @@ publications: install: pypi: muon conda: conda-forge::muon +primary_category: Multimodal tags: - multimodal - - multi-omics - - integration -topics: - - multi-omics - - integration - - preprocessing + - data integration license: BSD-3-Clause version: 0.1.7 contact: diff --git a/packages/nichepca/meta.yaml b/packages/nichepca/meta.yaml index 9a40f34b..7c887a93 100644 --- a/packages/nichepca/meta.yaml +++ b/packages/nichepca/meta.yaml @@ -6,12 +6,9 @@ documentation_home: https://nichepca.readthedocs.io/ tutorials_home: https://nichepca.readthedocs.io/page/notebooks/example.html install: pypi: nichepca +primary_category: Spatial tags: - - spatial-omics - - spatial domain identification - - spatial clustering -topics: - - spatial + - spatial transcriptomics - clustering license: MIT version: v0.0.3 diff --git a/packages/novae/meta.yaml b/packages/novae/meta.yaml index 8526ce90..b3f5362c 100644 --- a/packages/novae/meta.yaml +++ b/packages/novae/meta.yaml @@ -8,15 +8,10 @@ publications: - 10.1101/2024.09.09.612009 install: pypi: novae +primary_category: Spatial tags: - - spatial-omics - - spatial-transcriptomics - - spatialdata + - spatial transcriptomics - deep learning -topics: - - spatial - - clustering - - integration license: BSD-3-Clause version: v0.2.1 contact: diff --git a/packages/omicverse/meta.yaml b/packages/omicverse/meta.yaml index 6d1ef78f..e769387b 100644 --- a/packages/omicverse/meta.yaml +++ b/packages/omicverse/meta.yaml @@ -9,13 +9,10 @@ publications: - 10.1101/2023.06.06.543913 install: pypi: omicverse +primary_category: Multimodal tags: - - single-cell - - bulk-rna-seq - - omics - - bioinformatics -topics: - - multi-omics + - bulk RNA-seq + - multimodal license: GPL-3.0-only version: v1.4.12 contact: diff --git a/packages/palantir/meta.yaml b/packages/palantir/meta.yaml index 34541d5d..f1a60279 100644 --- a/packages/palantir/meta.yaml +++ b/packages/palantir/meta.yaml @@ -13,19 +13,11 @@ publications: - 10.1038/s41587-019-0068-4 install: pypi: palantir +primary_category: scRNA-seq tags: - - markov-chain - - dimensionality-reduction - - scrna-seq - - trajectory-generation - - diffusion-maps - - differentiation - - manifold-learning - - single-cell-genomics - - cell-fate-transitions - - scrna-seq-analysis -topics: - - trajectory + - scRNA-seq + - dimensionality reduction + - trajectory inference license: GPL-2.0-or-later version: v1.3.3 contact: diff --git a/packages/panpipes/meta.yaml b/packages/panpipes/meta.yaml index 81674a74..a99f224f 100644 --- a/packages/panpipes/meta.yaml +++ b/packages/panpipes/meta.yaml @@ -8,15 +8,11 @@ publications: - 10.1101/2023.03.11.532085 install: pypi: panpipes +primary_category: Multimodal tags: - - single-cell - - multiomics + - spatial transcriptomics + - multimodal - pipeline - - spatial - - bioinformatics -topics: - - multi-omics - - spatial license: BSD-3-Clause version: v0.5.0 contact: diff --git a/packages/pcdl/meta.yaml b/packages/pcdl/meta.yaml index f52ba9e7..cfec76ba 100644 --- a/packages/pcdl/meta.yaml +++ b/packages/pcdl/meta.yaml @@ -6,16 +6,9 @@ tutorials_home: https://github.com/elmbeech/physicelldataloader/blob/master/man/ install: pypi: pcdl license: BSD-3-Clause +primary_category: Infrastructure tags: - - python3 - - downstream data analysis - - physicell - - multicellular system - - agent-based modeling - - diffusion transport solver - - newtonian physics -topics: - - infrastructure + - file formats #publications: version: v4.0.4 category: ecosystem diff --git a/packages/pegasus/meta.yaml b/packages/pegasus/meta.yaml index 4a23fdbf..6a95d20e 100644 --- a/packages/pegasus/meta.yaml +++ b/packages/pegasus/meta.yaml @@ -8,12 +8,12 @@ publications: - 10.1038/s41592-020-0905-x install: pypi: pegasuspy +primary_category: scRNA-seq tags: - - transcriptome analysis -topics: + - scRNA-seq - preprocessing + - cell-type annotation - clustering - - annotation license: BSD-3-Clause version: v1.7.1 contact: diff --git a/packages/pertpy/meta.yaml b/packages/pertpy/meta.yaml index 8fc092f2..cf9adf20 100644 --- a/packages/pertpy/meta.yaml +++ b/packages/pertpy/meta.yaml @@ -11,14 +11,10 @@ publications: install: pypi: pertpy conda: conda-forge::pertpy +primary_category: scRNA-seq tags: + - differential expression - perturbation - - drug response - - CRISPR - - genetic perturbation -topics: - - perturbation - - differential-analysis license: MIT version: 1.0.3 contact: diff --git a/packages/popV/meta.yaml b/packages/popV/meta.yaml index ee897a2b..254b2f08 100644 --- a/packages/popV/meta.yaml +++ b/packages/popV/meta.yaml @@ -5,13 +5,10 @@ project_home: https://github.com/YosefLab/popV documentation_home: https://popv.readthedocs.io/ install: pypi: popv +primary_category: scRNA-seq tags: - - cell type labels - - batch integration - - automatic annotation -topics: - - annotation - - integration + - data integration + - cell-type annotation license: MIT version: v0.5.2 contact: diff --git a/packages/pyCrossTalkeR/meta.yaml b/packages/pyCrossTalkeR/meta.yaml index 7e923f13..47311ec3 100644 --- a/packages/pyCrossTalkeR/meta.yaml +++ b/packages/pyCrossTalkeR/meta.yaml @@ -6,13 +6,10 @@ documentation_home: https://pycrosstalker.readthedocs.io tutorials_home: https://pycrosstalker.readthedocs.io install: pypi: pycrosstalker +primary_category: scRNA-seq tags: - - CCI - - scRNAseq - - Node Importance -topics: - - cell-communication - - visualization + - scRNA-seq + - cell-cell communication license: MIT version: v2.1.0 contact: diff --git a/packages/pyLemur/meta.yaml b/packages/pyLemur/meta.yaml index f13e967e..c1752227 100644 --- a/packages/pyLemur/meta.yaml +++ b/packages/pyLemur/meta.yaml @@ -8,12 +8,9 @@ publications: - 10.1101/2023.03.06.531268 install: pypi: pyLemur +primary_category: scRNA-seq tags: - - single-cell - differential expression - - multi-condition -topics: - - differential-analysis license: MIT version: v0.1.0 contact: diff --git a/packages/pySCENIC/meta.yaml b/packages/pySCENIC/meta.yaml index a3dd8c2e..44fa0e4e 100644 --- a/packages/pySCENIC/meta.yaml +++ b/packages/pySCENIC/meta.yaml @@ -13,11 +13,9 @@ publications: - 10.1038/s41596-020-0336-2 install: pypi: pyscenic +primary_category: scRNA-seq tags: - - regulatory networks - - clustering -topics: - - gene-networks + - gene regulatory networks - clustering license: GPL-3.0-only version: v0.12.0 diff --git a/packages/pyUCell/meta.yaml b/packages/pyUCell/meta.yaml index 7c461a6a..ef729123 100644 --- a/packages/pyUCell/meta.yaml +++ b/packages/pyUCell/meta.yaml @@ -13,12 +13,9 @@ publications: - 10.1016/j.csbj.2021.06.043 install: pypi: pyucell +primary_category: scRNA-seq tags: - - single-cell - - signature scoring - - module scoring -topics: - - differential-analysis + - functional analysis license: MIT version: v0.3.0 contact: diff --git a/packages/pycea/meta.yaml b/packages/pycea/meta.yaml index a0b58c5c..3b0f253d 100644 --- a/packages/pycea/meta.yaml +++ b/packages/pycea/meta.yaml @@ -6,12 +6,10 @@ documentation_home: https://pycea.readthedocs.io/ tutorials_home: https://pycea.readthedocs.io/ install: pypi: pycea-lineage +primary_category: scRNA-seq tags: - - lineage-tracing - - TreeData -topics: - - trajectory - - visualization + - lineage tracing + - data structures license: BSD-3-Clause version: v0.1.0 contact: diff --git a/packages/pychromVAR/meta.yaml b/packages/pychromVAR/meta.yaml index 21c36e47..1f958372 100644 --- a/packages/pychromVAR/meta.yaml +++ b/packages/pychromVAR/meta.yaml @@ -6,11 +6,10 @@ documentation_home: https://pychromvar.readthedocs.io/ tutorials_home: https://pychromvar.readthedocs.io/ install: pypi: pychromvar +primary_category: Epigenomics tags: - - TF - - scATAC-seq -topics: - - epigenomics + - ATAC-seq + - gene regulatory networks license: MIT version: v0.0.3 contact: diff --git a/packages/pytximport/meta.yaml b/packages/pytximport/meta.yaml index 2074ad87..c563c30b 100644 --- a/packages/pytximport/meta.yaml +++ b/packages/pytximport/meta.yaml @@ -6,12 +6,11 @@ documentation_home: https://pytximport.readthedocs.io/ tutorials_home: https://pytximport.readthedocs.io/ install: pypi: pytximport +primary_category: bulk RNA-seq tags: - - rna-seq - - bulk-rna-seq - - differential-expression -topics: - - infrastructure + - bulk RNA-seq + - differential expression + - file formats license: GPL-3.0-only version: v0.2.0 contact: diff --git a/packages/rapids-singlecell/meta.yaml b/packages/rapids-singlecell/meta.yaml index ee4cefdc..d752bca2 100644 --- a/packages/rapids-singlecell/meta.yaml +++ b/packages/rapids-singlecell/meta.yaml @@ -7,14 +7,11 @@ documentation_home: https://rapids-singlecell.readthedocs.io/ tutorials_home: https://rapids-singlecell.readthedocs.io/page/tutorials.html install: pypi: rapids-singlecell +primary_category: scRNA-seq tags: - - GPU acceleration - - single-cell - - RAPIDS - - CUDA -topics: - preprocessing - clustering + - GPU acceleration license: MIT version: 0.13.3 contact: diff --git a/packages/scCellFie/meta.yaml b/packages/scCellFie/meta.yaml index 1a4c7303..64e7c5a0 100644 --- a/packages/scCellFie/meta.yaml +++ b/packages/scCellFie/meta.yaml @@ -6,16 +6,11 @@ documentation_home: https://sccellfie.readthedocs.io/ tutorials_home: https://sccellfie.readthedocs.io/ install: pypi: sccellfie +primary_category: scRNA-seq tags: - - single-cell - - spatial - - metabolism - - metabolic activities + - spatial transcriptomics + - functional analysis - cell-cell communication -topics: - - differential-analysis - - spatial - - cell-communication license: MIT version: v0.4.5 contact: diff --git a/packages/scDataLoader/meta.yaml b/packages/scDataLoader/meta.yaml index ef034351..ee96aa01 100644 --- a/packages/scDataLoader/meta.yaml +++ b/packages/scDataLoader/meta.yaml @@ -9,17 +9,12 @@ publications: - 10.1101/2024.07.29.605556 install: pypi: scdataloader +primary_category: Infrastructure tags: - - dataloader - - single cell - - RNAseq - - pytorch - - lightning - - cellxgene - - preprocessing -topics: - - infrastructure + - scRNA-seq - preprocessing + - deep learning + - file formats license: MIT version: v1.2.2 contact: diff --git a/packages/scFates/meta.yaml b/packages/scFates/meta.yaml index a6494ec5..b0a14b5d 100644 --- a/packages/scFates/meta.yaml +++ b/packages/scFates/meta.yaml @@ -8,12 +8,10 @@ publications: - 10.1093/bioinformatics/btac746 install: pypi: scFates +primary_category: scRNA-seq tags: + - trajectory inference - pseudotime - - cell-fate - - trajectory-generation -topics: - - trajectory license: BSD-3-Clause version: v1.0.0 contact: diff --git a/packages/scGen/meta.yaml b/packages/scGen/meta.yaml index 8f6db694..e5c54361 100644 --- a/packages/scGen/meta.yaml +++ b/packages/scGen/meta.yaml @@ -9,10 +9,9 @@ publications: - 10.1038/s41592-019-0494-8 install: pypi: scgen +primary_category: scRNA-seq tags: - perturbation -topics: - - perturbation license: GPL-3.0-only version: v2.1.0 contact: diff --git a/packages/scPRINT-2/meta.yaml b/packages/scPRINT-2/meta.yaml index 3d7791ef..422a54e8 100644 --- a/packages/scPRINT-2/meta.yaml +++ b/packages/scPRINT-2/meta.yaml @@ -7,25 +7,17 @@ publications: - 10.64898/2025.12.11.693702v2 install: pypi: scprint2 +primary_category: scRNA-seq tags: - - foundation model - - single cell - - RNAseq - - gene network inference + - scRNA-seq - denoising - - zero imputation - - label prediction - - zero shot - - embedding - - pytorch - - lightning - - species integration - - expression imputation - - counterfactual predictions -topics: - - gene-networks - - annotation - - preprocessing + - data integration + - cell-type annotation + - gene regulatory networks + - dimensionality reduction + - perturbation + - deep learning + - foundation model license: GPL-3.0-or-later version: v1.0.0 contact: diff --git a/packages/scPRINT/meta.yaml b/packages/scPRINT/meta.yaml index 60091de1..7920a12b 100644 --- a/packages/scPRINT/meta.yaml +++ b/packages/scPRINT/meta.yaml @@ -7,22 +7,15 @@ publications: - 10.1101/2024.07.29.605556 install: pypi: scprint +primary_category: scRNA-seq tags: - - foundation model - - single cell - - RNAseq - - gene network inference + - scRNA-seq - denoising - - zero imputation - - label prediction - - zero shot - - embedding - - pytorch - - lightning -topics: - - gene-networks - - annotation - - preprocessing + - cell-type annotation + - gene regulatory networks + - dimensionality reduction + - deep learning + - foundation model license: MIT version: v1.6.2 contact: diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml index b310e69a..a5d779d4 100644 --- a/packages/scXpand/meta.yaml +++ b/packages/scXpand/meta.yaml @@ -9,14 +9,11 @@ publications: - 10.1101/2025.09.14.676069 install: pypi: scxpand +primary_category: Adaptive immune cell receptor tags: - - cancer - scRNA-seq - - scTCR-seq - - T-cell clonal expansion - - machine learning -topics: - - immune + - immune receptor + - deep learning license: MIT version: v0.4.3 contact: diff --git a/packages/scanpro/meta.yaml b/packages/scanpro/meta.yaml index 266a9dc3..b6db01fb 100644 --- a/packages/scanpro/meta.yaml +++ b/packages/scanpro/meta.yaml @@ -7,12 +7,10 @@ publications: - 10.1101/2023.08.14.553234 install: pypi: scanpro +primary_category: scRNA-seq tags: - - single cell - - proportion analysis - - multi omics -topics: - - differential-analysis + - multimodal + - compositional analysis license: MIT version: 0.2.0 contact: diff --git a/packages/scanpy/meta.yaml b/packages/scanpy/meta.yaml index c7722b91..4d415418 100644 --- a/packages/scanpy/meta.yaml +++ b/packages/scanpy/meta.yaml @@ -12,16 +12,11 @@ publications: install: pypi: scanpy conda: conda-forge::scanpy +primary_category: scRNA-seq tags: - - single-cell - preprocessing - - clustering - - visualization - differential expression -topics: - - preprocessing - clustering - - differential-analysis - visualization license: BSD-3-Clause version: 1.11.5 diff --git a/packages/schist/meta.yaml b/packages/schist/meta.yaml index 3f430d8c..e2a07b76 100644 --- a/packages/schist/meta.yaml +++ b/packages/schist/meta.yaml @@ -6,11 +6,9 @@ tutorials_home: https://schist.readthedocs.io/page/tutorials.html install: conda: conda-forge::schist license: BSD-3-Clause +primary_category: scRNA-seq tags: - clustering - - single-cell -topics: - - clustering publications: - 10.1186/s12859-021-04489-7 version: v0.8.1 diff --git a/packages/scib-rapids/meta.yaml b/packages/scib-rapids/meta.yaml index 40b50748..5d7511ac 100644 --- a/packages/scib-rapids/meta.yaml +++ b/packages/scib-rapids/meta.yaml @@ -6,14 +6,11 @@ project_home: https://github.com/maarten-devries/scib-rapids documentation_home: https://scib-rapids.readthedocs.io/ install: pypi: scib-rapids +primary_category: scRNA-seq tags: - - benchmarking - - single-cell - data integration + - benchmarking - GPU acceleration - - RAPIDS -topics: - - integration license: BSD-3-Clause version: 0.1.0 contact: diff --git a/packages/scib/meta.yaml b/packages/scib/meta.yaml index 7ad2514b..c5ea990a 100644 --- a/packages/scib/meta.yaml +++ b/packages/scib/meta.yaml @@ -7,12 +7,10 @@ publications: - 10.1038/s41592-021-01336-8 install: pypi: scib +primary_category: scRNA-seq tags: - - benchmarking - - single cell - data integration -topics: - - integration + - benchmarking license: MIT version: v1.0.5 contact: diff --git a/packages/scirpy/meta.yaml b/packages/scirpy/meta.yaml index 7e88404b..d6a0f30e 100644 --- a/packages/scirpy/meta.yaml +++ b/packages/scirpy/meta.yaml @@ -11,13 +11,9 @@ publications: install: pypi: scirpy conda: bioconda::scirpy +primary_category: Adaptive immune cell receptor tags: - immune receptor - - TCR - - BCR - - AIRR -topics: - - immune license: BSD-3-Clause version: 0.22.3 contact: diff --git a/packages/scmcp/meta.yaml b/packages/scmcp/meta.yaml index 1ded0ef3..42db75b1 100644 --- a/packages/scmcp/meta.yaml +++ b/packages/scmcp/meta.yaml @@ -4,13 +4,9 @@ project_home: https://github.com/scmcphub documentation_home: https://docs.scmcphub.org install: pypi: scmcp +primary_category: Infrastructure tags: - - scRNA-seq - - bioinformatics - - LLM - - AI -topics: - - infrastructure + - large language models license: BSD-3-Clause version: v0.2.2 contact: diff --git a/packages/sctriangulate/meta.yaml b/packages/sctriangulate/meta.yaml index 983e079a..10611596 100644 --- a/packages/sctriangulate/meta.yaml +++ b/packages/sctriangulate/meta.yaml @@ -8,10 +8,9 @@ publications: - 10.1101/2021.10.16.464640 install: pypi: sctriangulate +primary_category: scRNA-seq tags: - clustering -topics: - - clustering license: MIT version: v0.12.0 contact: diff --git a/packages/scvelo/meta.yaml b/packages/scvelo/meta.yaml index 2063278b..eba2ea52 100644 --- a/packages/scvelo/meta.yaml +++ b/packages/scvelo/meta.yaml @@ -7,10 +7,9 @@ publications: - 10.1038/s41587-020-0591-3 install: pypi: scvelo +primary_category: scRNA-seq tags: - - rna velocity -topics: - - trajectory + - RNA velocity license: BSD-3-Clause version: v0.2.5 contact: diff --git a/packages/scverse-tutorials/meta.yaml b/packages/scverse-tutorials/meta.yaml index 3b0cc1e9..7bcd9c98 100644 --- a/packages/scverse-tutorials/meta.yaml +++ b/packages/scverse-tutorials/meta.yaml @@ -4,12 +4,9 @@ description: | project_home: https://github.com/scverse/scverse-tutorials documentation_home: https://scverse-tutorials.readthedocs.io/ tutorials_home: https://scverse-tutorials.readthedocs.io/ +primary_category: Infrastructure tags: - - tutorials - - education - documentation -topics: - - infrastructure license: BSD-3-Clause contact: - grst diff --git a/packages/scverse.github.io/meta.yaml b/packages/scverse.github.io/meta.yaml index a27d8a0c..56cd38ac 100644 --- a/packages/scverse.github.io/meta.yaml +++ b/packages/scverse.github.io/meta.yaml @@ -3,11 +3,9 @@ description: | scverse.org website project_home: https://github.com/scverse/scverse.github.io documentation_home: https://scverse.org +primary_category: Infrastructure tags: - - website - documentation -topics: - - infrastructure license: BSD-3-Clause authors: - gtca diff --git a/packages/scvi-tools/meta.yaml b/packages/scvi-tools/meta.yaml index 23ecd4c0..e733b18f 100644 --- a/packages/scvi-tools/meta.yaml +++ b/packages/scvi-tools/meta.yaml @@ -29,15 +29,13 @@ publications: install: pypi: scvi-tools conda: conda-forge::scvi-tools +primary_category: scRNA-seq tags: - - machine learning - - probabilistic models - - variational inference + - data integration + - cell-type annotation + - differential expression - deep learning -topics: - - integration - - annotation - - differential-analysis + - probabilistic modeling license: BSD-3-Clause version: 1.4.0.post1 contact: diff --git a/packages/scxmatch/meta.yaml b/packages/scxmatch/meta.yaml index ccca5753..981b94b1 100644 --- a/packages/scxmatch/meta.yaml +++ b/packages/scxmatch/meta.yaml @@ -9,17 +9,11 @@ publications: - 10.1101/2025.06.25.661473 install: conda: bioconda::scxmatch +primary_category: scRNA-seq tags: - scRNA-seq - - single-cell - - python - - statistical testing - - distance-based matching - perturbation - - condition -topics: - - perturbation - - differential-analysis + - probabilistic modeling license: MIT version: v0.1.0 contact: diff --git a/packages/scyan/meta.yaml b/packages/scyan/meta.yaml index b9b5afe7..85c6220f 100644 --- a/packages/scyan/meta.yaml +++ b/packages/scyan/meta.yaml @@ -10,15 +10,11 @@ publications: - 10.1093/bib/bbad260 install: pypi: scyan +primary_category: Proteomics tags: - - cytometry - - annotation - - batch-effect correction - - debarcoding -topics: - - proteomics - - annotation - - integration + - flow cytometry + - data integration + - cell-type annotation license: BSD-3-Clause version: v1.5.0 contact: diff --git a/packages/sift-sc/meta.yaml b/packages/sift-sc/meta.yaml index 41d092e8..849296de 100644 --- a/packages/sift-sc/meta.yaml +++ b/packages/sift-sc/meta.yaml @@ -7,11 +7,8 @@ documentation_home: https://sift-sc.readthedocs.io/ tutorials_home: https://sift-sc.readthedocs.io/ install: pypi: sift-sc +primary_category: scRNA-seq tags: - - single-cell - - signals - - filter -topics: - preprocessing license: BSD-3-Clause version: v0.1.0 diff --git a/packages/sincei/meta.yaml b/packages/sincei/meta.yaml index 3f0dccad..d359f20e 100644 --- a/packages/sincei/meta.yaml +++ b/packages/sincei/meta.yaml @@ -11,19 +11,15 @@ publications: - 10.1101/2024.07.27.605424 install: pypi: sincei +primary_category: Epigenomics tags: - - single-cell + - epigenomics + - multimodal - preprocessing - quality control - clustering - visualization - - epigenomics - - multi omics - - BAM -topics: - - epigenomics - - preprocessing - - clustering + - file formats license: MIT version: v0.5.1 authors: diff --git a/packages/sobolev-alignment/meta.yaml b/packages/sobolev-alignment/meta.yaml index 4c3bbe1d..7bf0c2ed 100644 --- a/packages/sobolev-alignment/meta.yaml +++ b/packages/sobolev-alignment/meta.yaml @@ -7,15 +7,11 @@ publications: - 10.1101/2022.03.08.483431 install: pypi: sobolev-alignment +primary_category: scRNA-seq tags: - - ML - - deep-generative-models - - kernel-methods - - pre-clinical - - clinical - - scrnaseq -topics: - - integration + - scRNA-seq + - deep learning + - probabilistic modeling license: MIT version: 1.0.0 contact: diff --git a/packages/sopa/meta.yaml b/packages/sopa/meta.yaml index 5b4beeee..5bfa88bd 100644 --- a/packages/sopa/meta.yaml +++ b/packages/sopa/meta.yaml @@ -9,15 +9,11 @@ publications: - 10.1038/s41467-024-48981-z install: pypi: sopa +primary_category: Spatial tags: - - spatial-omics - - spatial-transcriptomics - - multiplex imaging - - spatialdata - - pipeline -topics: - - spatial + - spatial transcriptomics - imaging + - pipeline license: BSD-3-Clause version: v1.0.0 contact: diff --git a/packages/spatial-eggplant/meta.yaml b/packages/spatial-eggplant/meta.yaml index 37982f57..a691c61a 100644 --- a/packages/spatial-eggplant/meta.yaml +++ b/packages/spatial-eggplant/meta.yaml @@ -8,12 +8,10 @@ publications: - 10.1101/2021.11.11.468178 install: pypi: spatial-eggplant +primary_category: Spatial tags: - - spatial alignment - - spatial registration -topics: - - spatial - - integration + - spatial transcriptomics + - data integration license: MIT version: v0.2.3 contact: diff --git a/packages/spatialdata/meta.yaml b/packages/spatialdata/meta.yaml index b91effe9..c6d218e3 100644 --- a/packages/spatialdata/meta.yaml +++ b/packages/spatialdata/meta.yaml @@ -10,13 +10,11 @@ publications: - 10.1038/s41592-024-02212-x install: pypi: spatialdata +primary_category: Data structures tags: - - data structure - - spatial omics - - FAIR -topics: - - spatial - - infrastructure + - spatial transcriptomics + - data structures + - file formats license: BSD-3-Clause version: 0.5.0 contact: diff --git a/packages/spatialproteomics/meta.yaml b/packages/spatialproteomics/meta.yaml index 6d6cdd9c..8a160ecc 100644 --- a/packages/spatialproteomics/meta.yaml +++ b/packages/spatialproteomics/meta.yaml @@ -8,16 +8,12 @@ documentation_home: https://sagar87.github.io/spatialproteomics tutorials_home: https://sagar87.github.io/spatialproteomics/notebooks/ExampleWorkflow.html install: pypi: spatialproteomics +primary_category: Spatial tags: - - spatial-omics - - spatial-proteomics - - multiplex imaging - - spatialdata - - pipeline -topics: - - spatial - - proteomics + - spatial transcriptomics + - spatial proteomics - imaging + - pipeline license: MIT version: v0.7.0 contact: diff --git a/packages/spatiomic/meta.yaml b/packages/spatiomic/meta.yaml index e1083d37..604fbeb4 100644 --- a/packages/spatiomic/meta.yaml +++ b/packages/spatiomic/meta.yaml @@ -6,18 +6,12 @@ documentation_home: https://spatiomic.org tutorials_home: https://spatiomic.org/latest/tutorials/full_example.html install: pypi: spatiomic +primary_category: Spatial tags: - - spatial biology + - spatial transcriptomics - spatial proteomics - - spatial omics - - multiplexed protein imaging - - PathoPlex - - subcellular analysis -topics: - - spatial - - proteomics - imaging - - clustering + - segmentation license: GPL-3.0-only version: v0.5.0 contact: diff --git a/packages/squidpy/meta.yaml b/packages/squidpy/meta.yaml index b3a11e2c..9817c493 100644 --- a/packages/squidpy/meta.yaml +++ b/packages/squidpy/meta.yaml @@ -12,14 +12,10 @@ publications: install: pypi: squidpy conda: conda-forge::squidpy +primary_category: Spatial tags: - - spatial omics - spatial transcriptomics - - image analysis -topics: - - spatial - imaging - - visualization license: BSD-3-Clause version: 1.6.5 contact: diff --git a/packages/stats/meta.yaml b/packages/stats/meta.yaml index 0f215e40..8ee439f6 100644 --- a/packages/stats/meta.yaml +++ b/packages/stats/meta.yaml @@ -3,11 +3,9 @@ description: | Statistics for scverse project_home: https://github.com/scverse/stats documentation_home: https://scverse.org/stats/ +primary_category: Infrastructure tags: - - statistics - - metrics -topics: - - infrastructure + - benchmarking license: MIT authors: - maltekuehl diff --git a/packages/symphonypy/meta.yaml b/packages/symphonypy/meta.yaml index c4f1f7d5..146629a2 100644 --- a/packages/symphonypy/meta.yaml +++ b/packages/symphonypy/meta.yaml @@ -6,11 +6,9 @@ project_home: https://github.com/potulabe/symphonypy documentation_home: https://github.com/potulabe/symphonypy install: pypi: symphonypy +primary_category: scRNA-seq tags: - - label-transfer -topics: - - annotation - - integration + - cell-type annotation license: GPL-3.0-only version: v0.2.1 contact: diff --git a/packages/tangram/meta.yaml b/packages/tangram/meta.yaml index f2dd70b6..30c806e3 100644 --- a/packages/tangram/meta.yaml +++ b/packages/tangram/meta.yaml @@ -8,12 +8,10 @@ publications: - 10.1038/s41592-021-01264-7 install: pypi: tangram-sc +primary_category: Spatial tags: - - spatial decomposition - - spatial mapping -topics: - - spatial - - integration + - spatial transcriptomics + - deconvolution license: BSD-3-Clause version: v1.0.3 contact: diff --git a/packages/tau-community-detection/meta.yaml b/packages/tau-community-detection/meta.yaml index 050469aa..1241104f 100644 --- a/packages/tau-community-detection/meta.yaml +++ b/packages/tau-community-detection/meta.yaml @@ -9,14 +9,8 @@ documentation_home: https://github.com/HillelCharbit/TAU#readme install: pypi: tau-community-detection license: MIT +primary_category: scRNA-seq tags: - - community-detection - - clustering - - single-cell - - scanpy - - anndata - - graph-analysis -topics: - clustering publications: - 10.1093/pnasnexus/pgad180 diff --git a/packages/vitessce/meta.yaml b/packages/vitessce/meta.yaml index 00812f8d..322ee346 100644 --- a/packages/vitessce/meta.yaml +++ b/packages/vitessce/meta.yaml @@ -9,12 +9,12 @@ publications: - 10.1038/s41592-024-02436-x install: pypi: vitessce +primary_category: Spatial tags: + - spatial transcriptomics - imaging -topics: + - multimodal - visualization - - spatial - - imaging license: MIT version: v3.5.7 contact: diff --git a/packages/wsidata/meta.yaml b/packages/wsidata/meta.yaml index 8932877b..6deda37c 100644 --- a/packages/wsidata/meta.yaml +++ b/packages/wsidata/meta.yaml @@ -5,12 +5,11 @@ project_home: https://github.com/rendeirolab/wsidata documentation_home: https://wsidata.readthedocs.io/ install: pypi: wsidata +primary_category: Data structures tags: - - Pathology - - Whole Slide Imaging -topics: - imaging - - infrastructure + - data structures + - file formats license: MIT version: v0.3.0 contact: diff --git a/packages/zellkonverter/meta.yaml b/packages/zellkonverter/meta.yaml index 6161e467..6e470843 100644 --- a/packages/zellkonverter/meta.yaml +++ b/packages/zellkonverter/meta.yaml @@ -9,13 +9,11 @@ tutorials_home: https://theislab.github.io/zellkonverter/ install: bioconductor: zellkonverter license: MIT +language: R +primary_category: Data structures tags: - data structures - interoperability - - R - - Bioconductor -topics: - - infrastructure version: 1.20.0 contact: - lazappi diff --git a/scripts/src/ecosystem_scripts/schema.json b/scripts/src/ecosystem_scripts/schema.json index 02643a73..87bab1ea 100644 --- a/scripts/src/ecosystem_scripts/schema.json +++ b/scripts/src/ecosystem_scripts/schema.json @@ -186,45 +186,85 @@ "ZPL-2.1" ] }, - "tags": { - "description": "Keywords that describe the package", - "type": "array", - "items": { - "type": "string" - }, - "minItems": 1, - "uniqueItems": true + "primary_category": { + "description": "The single category the package is listed under on scverse.org/packages. Pick the one a user looking for this package would browse first.", + "type": "string", + "enum": [ + "Data structures", + "scRNA-seq", + "bulk RNA-seq", + "Spatial", + "Epigenomics", + "Proteomics", + "Adaptive immune cell receptor", + "Multimodal", + "Imaging", + "Infrastructure" + ] }, - "topics": { - "description": "What the package is for, from a controlled vocabulary. Drives the filters on scverse.org/packages. Pick every topic that genuinely applies, usually one to three. Propose additions in a pull request.", + "tags": { + "description": "What the package does, from a controlled vocabulary. Used for filtering and search on scverse.org/packages. Pick every tag that genuinely applies. If none of them fit, add a term to this enum in your pull request.", "type": "array", "items": { "type": "string", "enum": [ - "annotation", - "cell-communication", - "clustering", - "deconvolution", - "differential-analysis", + "scRNA-seq", + "bulk RNA-seq", + "spatial transcriptomics", + "spatial proteomics", + "proteomics", + "flow cytometry", + "ATAC-seq", "epigenomics", - "gene-networks", + "immune receptor", "imaging", - "immune", - "infrastructure", - "integration", - "multi-omics", - "perturbation", + "multimodal", "preprocessing", - "proteomics", - "spatial", - "trajectory", - "visualization" + "quality control", + "denoising", + "data integration", + "cell-type annotation", + "differential expression", + "compositional analysis", + "functional analysis", + "gene regulatory networks", + "cell-cell communication", + "deconvolution", + "clustering", + "dimensionality reduction", + "trajectory inference", + "pseudotime", + "RNA velocity", + "lineage tracing", + "perturbation", + "spatially variable genes", + "segmentation", + "copy number variation", + "visualization", + "benchmarking", + "deep learning", + "foundation model", + "large language models", + "probabilistic modeling", + "optimal transport", + "GPU acceleration", + "pipeline", + "data structures", + "interoperability", + "file formats", + "documentation" ] }, "minItems": 1, - "maxItems": 4, + "maxItems": 10, "uniqueItems": true }, + "language": { + "description": "Language a user writes code in when using the package. Assumed to be Python when omitted.", + "type": "string", + "default": "Python", + "enum": ["Python", "R", "Julia", "Rust"] + }, "publications": { "description": "DOIs of publications describing the package", "type": "array", @@ -274,7 +314,7 @@ "documentation_home", "license", "tags", - "topics", + "primary_category", "category" ], "if": { From 0c98279cd25fbb5a51cdef4e18791bc00e652cb5 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Thu, 13 Aug 2026 10:21:59 +0200 Subject: [PATCH 4/6] Trim editorializing from the README --- README.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index cc8c3d9e..ebd96f26 100644 --- a/README.md +++ b/README.md @@ -24,8 +24,8 @@ Submit a pull-request adding a `meta.yaml` file for your package to the `package ## Categories, tags and language -Keywords are a controlled vocabulary rather than free text, so that the same concept is not spelled three different ways across the registry. -The vocabulary is defined in [`schema.json`](scripts/src/ecosystem_scripts/schema.json) and validated in CI, and it deliberately overlaps with the one used by the [tutorial registry](https://github.com/scverse/scverse-tutorials/blob/main/tutorial-registry/schema.json). +Keywords come from a controlled vocabulary, defined in [`schema.json`](scripts/src/ecosystem_scripts/schema.json) and validated in CI. +It overlaps with the vocabulary used by the [tutorial registry](https://github.com/scverse/scverse-tutorials/blob/main/tutorial-registry/schema.json). `primary_category` is the single category your package is listed under on [scverse.org/packages](https://scverse.org/packages/#ecosystem). Pick the one a user looking for your package would browse first. @@ -49,11 +49,10 @@ Pick every tag that genuinely applies. - **How it is built** — `deep learning`, `foundation model`, `large language models`, `probabilistic modeling`, `optimal transport`, `GPU acceleration`, `pipeline` - **Project shape** — `data structures`, `interoperability`, `file formats`, `documentation` -If none of the existing terms fit your package, add one to the enum in your pull request and say why. -That is a deliberate speed bump: it keeps the vocabulary small enough to be useful, while letting it grow when the science does. +If none of the existing terms fit your package, add one to the enum in your pull request. `language` is the language you write in when using the package. -It is assumed to be `Python` when omitted, so only set it if that is wrong. +It is assumed to be `Python` when omitted. ## What are the requirements for an ecosystem package? From 2b10fdb6b44e08d5bd05fec5ee7aac6ac7654491 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Thu, 13 Aug 2026 10:23:16 +0200 Subject: [PATCH 5/6] Make language required rather than defaulting to Python A JSON Schema default is documentation, not behaviour: jsonschema does not apply it, so the field stays absent from packages.json and every consumer has to reimplement the fallback. Stating it on all 118 packages costs one line each and removes that. --- README.md | 3 +-- packages/AESTETIK/meta.yaml | 1 + packages/CellAnnotator/meta.yaml | 1 + packages/CellCharter/meta.yaml | 1 + packages/CellMapper/meta.yaml | 1 + packages/CellOracle/meta.yaml | 1 + packages/CellRank/meta.yaml | 1 + packages/Cell_BLAST/meta.yaml | 1 + packages/CellphoneDB/meta.yaml | 1 + packages/Cirrocumulus/meta.yaml | 1 + packages/DOTools_py/meta.yaml | 1 + packages/DRVI/meta.yaml | 1 + packages/DoubletDetection/meta.yaml | 1 + packages/GPTBioInsightor/meta.yaml | 1 + packages/GRnnData/meta.yaml | 1 + packages/LazySlide/meta.yaml | 1 + packages/Mowgli/meta.yaml | 1 + packages/Multivelo/meta.yaml | 1 + packages/PEAKQC/meta.yaml | 1 + packages/PILOT/meta.yaml | 1 + packages/ParTIpy/meta.yaml | 1 + packages/PathML/meta.yaml | 1 + packages/PyDESeq2/meta.yaml | 1 + packages/Rectangle/meta.yaml | 1 + packages/SC2Spa/meta.yaml | 1 + packages/SCALEX/meta.yaml | 1 + packages/STMiner/meta.yaml | 1 + packages/SnapATAC2/meta.yaml | 1 + packages/TreeData/meta.yaml | 1 + packages/alphapepttools/meta.yaml | 1 + packages/anndata/meta.yaml | 1 + packages/annsel/meta.yaml | 1 + packages/benGRN/meta.yaml | 1 + packages/bento-tools/meta.yaml | 1 + packages/biolord/meta.yaml | 1 + packages/cell2location/meta.yaml | 1 + packages/cellxgene/meta.yaml | 1 + packages/clone2vec/meta.yaml | 1 + packages/cookiecutter-scverse/meta.yaml | 1 + packages/dandelion/meta.yaml | 1 + packages/decoupler/meta.yaml | 1 + packages/delnx/meta.yaml | 1 + packages/dvp-io/meta.yaml | 1 + packages/dynamo-release/meta.yaml | 1 + packages/ecosystem-packages/meta.yaml | 1 + packages/epiScanpy/meta.yaml | 1 + packages/eschr/meta.yaml | 1 + packages/favapy/meta.yaml | 1 + packages/flashdeconv/meta.yaml | 1 + packages/flowsom/meta.yaml | 1 + packages/governance/meta.yaml | 1 + packages/grassp/meta.yaml | 1 + packages/gssnng/meta.yaml | 1 + packages/hotspot/meta.yaml | 1 + packages/illico/meta.yaml | 1 + packages/infercnvpy/meta.yaml | 1 + packages/integration-testing/meta.yaml | 1 + packages/kompot/meta.yaml | 1 + packages/liana/meta.yaml | 1 + packages/maxspin/meta.yaml | 1 + packages/moscot/meta.yaml | 1 + packages/mudata/meta.yaml | 1 + packages/muon/meta.yaml | 1 + packages/nichepca/meta.yaml | 1 + packages/novae/meta.yaml | 1 + packages/omicverse/meta.yaml | 1 + packages/palantir/meta.yaml | 1 + packages/panpipes/meta.yaml | 1 + packages/pcdl/meta.yaml | 1 + packages/pegasus/meta.yaml | 1 + packages/pertpy/meta.yaml | 1 + packages/popV/meta.yaml | 1 + packages/pyCrossTalkeR/meta.yaml | 1 + packages/pyLemur/meta.yaml | 1 + packages/pySCENIC/meta.yaml | 1 + packages/pyUCell/meta.yaml | 1 + packages/pycea/meta.yaml | 1 + packages/pychromVAR/meta.yaml | 1 + packages/pytximport/meta.yaml | 1 + packages/rapids-singlecell/meta.yaml | 1 + packages/scCellFie/meta.yaml | 1 + packages/scDataLoader/meta.yaml | 1 + packages/scFates/meta.yaml | 1 + packages/scGen/meta.yaml | 1 + packages/scPRINT-2/meta.yaml | 1 + packages/scPRINT/meta.yaml | 1 + packages/scXpand/meta.yaml | 1 + packages/scanpro/meta.yaml | 1 + packages/scanpy/meta.yaml | 1 + packages/schist/meta.yaml | 1 + packages/scib-rapids/meta.yaml | 1 + packages/scib/meta.yaml | 1 + packages/scirpy/meta.yaml | 1 + packages/scmcp/meta.yaml | 1 + packages/sctriangulate/meta.yaml | 1 + packages/scvelo/meta.yaml | 1 + packages/scverse-tutorials/meta.yaml | 1 + packages/scverse.github.io/meta.yaml | 1 + packages/scvi-tools/meta.yaml | 1 + packages/scxmatch/meta.yaml | 1 + packages/scyan/meta.yaml | 1 + packages/sift-sc/meta.yaml | 1 + packages/sincei/meta.yaml | 1 + packages/sobolev-alignment/meta.yaml | 1 + packages/sopa/meta.yaml | 1 + packages/spatial-eggplant/meta.yaml | 1 + packages/spatialdata/meta.yaml | 1 + packages/spatialproteomics/meta.yaml | 1 + packages/spatiomic/meta.yaml | 1 + packages/squidpy/meta.yaml | 1 + packages/stats/meta.yaml | 1 + packages/symphonypy/meta.yaml | 1 + packages/tangram/meta.yaml | 1 + packages/tau-community-detection/meta.yaml | 1 + packages/vitessce/meta.yaml | 1 + packages/wsidata/meta.yaml | 1 + scripts/src/ecosystem_scripts/schema.json | 4 ++-- 117 files changed, 118 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index ebd96f26..0ab78e83 100644 --- a/README.md +++ b/README.md @@ -51,8 +51,7 @@ Pick every tag that genuinely applies. If none of the existing terms fit your package, add one to the enum in your pull request. -`language` is the language you write in when using the package. -It is assumed to be `Python` when omitted. +`language` is the language you write in when using the package: `Python`, `R`, `Julia` or `Rust`. ## What are the requirements for an ecosystem package? diff --git a/packages/AESTETIK/meta.yaml b/packages/AESTETIK/meta.yaml index 44e806ea..9622cac8 100644 --- a/packages/AESTETIK/meta.yaml +++ b/packages/AESTETIK/meta.yaml @@ -20,6 +20,7 @@ tags: - dimensionality reduction - deep learning license: MIT +language: Python version: v0.3.1 contact: - KalinNonchev diff --git a/packages/CellAnnotator/meta.yaml b/packages/CellAnnotator/meta.yaml index f4263a05..4e9357cc 100644 --- a/packages/CellAnnotator/meta.yaml +++ b/packages/CellAnnotator/meta.yaml @@ -10,6 +10,7 @@ tags: - cell-type annotation - large language models license: MIT +language: Python version: v0.1.3 contact: - Marius1311 diff --git a/packages/CellCharter/meta.yaml b/packages/CellCharter/meta.yaml index 9f005ed4..5c49062d 100644 --- a/packages/CellCharter/meta.yaml +++ b/packages/CellCharter/meta.yaml @@ -14,6 +14,7 @@ tags: - clustering - probabilistic modeling license: BSD-3-Clause +language: Python version: v0.3.1 contact: - marcovarrone diff --git a/packages/CellMapper/meta.yaml b/packages/CellMapper/meta.yaml index be88c3bd..272c9d0b 100644 --- a/packages/CellMapper/meta.yaml +++ b/packages/CellMapper/meta.yaml @@ -10,6 +10,7 @@ tags: - data integration - GPU acceleration license: MIT +language: Python version: v0.1.2 contact: - Marius1311 diff --git a/packages/CellOracle/meta.yaml b/packages/CellOracle/meta.yaml index caa9819e..2b6a0b36 100644 --- a/packages/CellOracle/meta.yaml +++ b/packages/CellOracle/meta.yaml @@ -15,6 +15,7 @@ tags: - gene regulatory networks - perturbation license: Apache-2.0 +language: Python version: v0.10.12 contact: - KenjiKamimoto-ac diff --git a/packages/CellRank/meta.yaml b/packages/CellRank/meta.yaml index 4ec95486..5ca5afbf 100644 --- a/packages/CellRank/meta.yaml +++ b/packages/CellRank/meta.yaml @@ -16,6 +16,7 @@ tags: - RNA velocity - deep learning license: BSD-3-Clause +language: Python version: v1.5.1 contact: - Marius1311 diff --git a/packages/Cell_BLAST/meta.yaml b/packages/Cell_BLAST/meta.yaml index 858ba1ce..a1f3718e 100644 --- a/packages/Cell_BLAST/meta.yaml +++ b/packages/Cell_BLAST/meta.yaml @@ -12,6 +12,7 @@ tags: - data integration - cell-type annotation license: MIT +language: Python version: v0.3.8 contact: - Jeff1995 diff --git a/packages/CellphoneDB/meta.yaml b/packages/CellphoneDB/meta.yaml index 54670f1c..d00ba793 100644 --- a/packages/CellphoneDB/meta.yaml +++ b/packages/CellphoneDB/meta.yaml @@ -16,6 +16,7 @@ tags: - scRNA-seq - cell-cell communication license: MIT +language: Python version: v5.0.0 contact: - chapuzzo diff --git a/packages/Cirrocumulus/meta.yaml b/packages/Cirrocumulus/meta.yaml index 8ed16591..b6b753eb 100644 --- a/packages/Cirrocumulus/meta.yaml +++ b/packages/Cirrocumulus/meta.yaml @@ -12,6 +12,7 @@ primary_category: scRNA-seq tags: - visualization license: BSD-3-Clause +language: Python version: v1.1.41 contact: - joshua-gould diff --git a/packages/DOTools_py/meta.yaml b/packages/DOTools_py/meta.yaml index 7b9ff8fc..48e85c49 100644 --- a/packages/DOTools_py/meta.yaml +++ b/packages/DOTools_py/meta.yaml @@ -10,6 +10,7 @@ tags: - scRNA-seq - visualization license: MIT +language: Python version: v0.0.2 contact: - davidrm-bio diff --git a/packages/DRVI/meta.yaml b/packages/DRVI/meta.yaml index 41ff3a0c..57d93886 100644 --- a/packages/DRVI/meta.yaml +++ b/packages/DRVI/meta.yaml @@ -19,6 +19,7 @@ tags: - deep learning - probabilistic modeling license: BSD-3-Clause +language: Python version: 0.2.0 contact: - moinfar diff --git a/packages/DoubletDetection/meta.yaml b/packages/DoubletDetection/meta.yaml index 602618b0..c94b2c9f 100644 --- a/packages/DoubletDetection/meta.yaml +++ b/packages/DoubletDetection/meta.yaml @@ -13,6 +13,7 @@ primary_category: scRNA-seq tags: - quality control license: MIT +language: Python version: v4.2 contact: - adamgayoso diff --git a/packages/GPTBioInsightor/meta.yaml b/packages/GPTBioInsightor/meta.yaml index 40a9e675..d00c5de5 100644 --- a/packages/GPTBioInsightor/meta.yaml +++ b/packages/GPTBioInsightor/meta.yaml @@ -11,6 +11,7 @@ tags: - deep learning - large language models license: BSD-3-Clause +language: Python version: v0.3.0 contact: - huangsh diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index 36204a32..24713424 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -14,6 +14,7 @@ tags: - gene regulatory networks - file formats license: MIT +language: Python version: v1.1.4 contact: - jkobject diff --git a/packages/LazySlide/meta.yaml b/packages/LazySlide/meta.yaml index 35bd0db9..7f7087c4 100644 --- a/packages/LazySlide/meta.yaml +++ b/packages/LazySlide/meta.yaml @@ -12,6 +12,7 @@ tags: - segmentation - deep learning license: MIT +language: Python version: v0.3.0 contact: - Mr-Milk diff --git a/packages/Mowgli/meta.yaml b/packages/Mowgli/meta.yaml index 54373a65..2a95645b 100644 --- a/packages/Mowgli/meta.yaml +++ b/packages/Mowgli/meta.yaml @@ -14,6 +14,7 @@ tags: - dimensionality reduction - optimal transport license: GPL-3.0-only +language: Python version: v0.2.0 contact: - gjhuizing diff --git a/packages/Multivelo/meta.yaml b/packages/Multivelo/meta.yaml index 1206831a..153b3846 100644 --- a/packages/Multivelo/meta.yaml +++ b/packages/Multivelo/meta.yaml @@ -14,6 +14,7 @@ tags: - epigenomics - RNA velocity license: BSD-3-Clause +language: Python version: 0.1.3 contact: - jw156605 diff --git a/packages/PEAKQC/meta.yaml b/packages/PEAKQC/meta.yaml index 0c903e6d..0078cb76 100644 --- a/packages/PEAKQC/meta.yaml +++ b/packages/PEAKQC/meta.yaml @@ -11,6 +11,7 @@ tags: - ATAC-seq - quality control license: MIT +language: Python version: 0.1.3 contact: - mlooso diff --git a/packages/PILOT/meta.yaml b/packages/PILOT/meta.yaml index d74b9bee..1ceee1ee 100644 --- a/packages/PILOT/meta.yaml +++ b/packages/PILOT/meta.yaml @@ -22,6 +22,7 @@ tags: - trajectory inference - optimal transport license: MIT +language: Python version: v2.0.6 contact: - mehdijoodaki diff --git a/packages/ParTIpy/meta.yaml b/packages/ParTIpy/meta.yaml index d0ee7097..7d9a5f68 100644 --- a/packages/ParTIpy/meta.yaml +++ b/packages/ParTIpy/meta.yaml @@ -7,6 +7,7 @@ tutorials_home: https://partipy.readthedocs.io/ install: pypi: partipy license: MIT +language: Python primary_category: scRNA-seq tags: - dimensionality reduction diff --git a/packages/PathML/meta.yaml b/packages/PathML/meta.yaml index fccce163..9e1e613b 100644 --- a/packages/PathML/meta.yaml +++ b/packages/PathML/meta.yaml @@ -12,6 +12,7 @@ primary_category: Imaging tags: - imaging license: GPL-2.0-only +language: Python version: v2.1.0 contact: - jacob-rosenthal diff --git a/packages/PyDESeq2/meta.yaml b/packages/PyDESeq2/meta.yaml index df28fcb3..944d6232 100644 --- a/packages/PyDESeq2/meta.yaml +++ b/packages/PyDESeq2/meta.yaml @@ -8,6 +8,7 @@ tutorials_home: https://pydeseq2.readthedocs.io/page/auto_examples/ install: pypi: pydeseq2 license: MIT +language: Python primary_category: bulk RNA-seq tags: - bulk RNA-seq diff --git a/packages/Rectangle/meta.yaml b/packages/Rectangle/meta.yaml index 23b29c5b..754e12fe 100644 --- a/packages/Rectangle/meta.yaml +++ b/packages/Rectangle/meta.yaml @@ -8,6 +8,7 @@ tutorials_home: https://rectanglepy.readthedocs.io/notebooks/example.html install: pypi: rectanglepy license: MIT +language: Python primary_category: bulk RNA-seq tags: - bulk RNA-seq diff --git a/packages/SC2Spa/meta.yaml b/packages/SC2Spa/meta.yaml index 09da8f8d..ac5bb516 100644 --- a/packages/SC2Spa/meta.yaml +++ b/packages/SC2Spa/meta.yaml @@ -16,6 +16,7 @@ tags: - cell-cell communication - deep learning license: BSD-3-Clause +language: Python version: v1.2 contact: - linbuliao diff --git a/packages/SCALEX/meta.yaml b/packages/SCALEX/meta.yaml index 49a62ecb..cb64c067 100644 --- a/packages/SCALEX/meta.yaml +++ b/packages/SCALEX/meta.yaml @@ -13,6 +13,7 @@ tags: - ATAC-seq - data integration license: MIT +language: Python version: v1.0.3 contact: - jsxlei diff --git a/packages/STMiner/meta.yaml b/packages/STMiner/meta.yaml index 3cf65fba..b35a7107 100644 --- a/packages/STMiner/meta.yaml +++ b/packages/STMiner/meta.yaml @@ -12,6 +12,7 @@ tags: - deep learning - optimal transport license: GPL-3.0-or-later +language: Python version: v1.1.0 contact: - PSSUN diff --git a/packages/SnapATAC2/meta.yaml b/packages/SnapATAC2/meta.yaml index 13d6a766..40948cd8 100644 --- a/packages/SnapATAC2/meta.yaml +++ b/packages/SnapATAC2/meta.yaml @@ -16,6 +16,7 @@ tags: - ATAC-seq - epigenomics license: MIT +language: Python version: 2.5.0 contact: - kaizhang diff --git a/packages/TreeData/meta.yaml b/packages/TreeData/meta.yaml index 305aaa49..50b2f923 100644 --- a/packages/TreeData/meta.yaml +++ b/packages/TreeData/meta.yaml @@ -12,6 +12,7 @@ tags: - lineage tracing - data structures license: BSD-3-Clause +language: Python version: v0.2.2 contact: - colganwi diff --git a/packages/alphapepttools/meta.yaml b/packages/alphapepttools/meta.yaml index d8282ad1..eb2bbf58 100644 --- a/packages/alphapepttools/meta.yaml +++ b/packages/alphapepttools/meta.yaml @@ -15,6 +15,7 @@ tags: - proteomics - file formats license: Apache-2.0 +language: Python version: 0.2.0 contact: - vbrennsteiner diff --git a/packages/anndata/meta.yaml b/packages/anndata/meta.yaml index 95dac8de..a53aa326 100644 --- a/packages/anndata/meta.yaml +++ b/packages/anndata/meta.yaml @@ -15,6 +15,7 @@ primary_category: Data structures tags: - data structures license: BSD-3-Clause +language: Python version: 0.12.4 contact: - flying-sheep diff --git a/packages/annsel/meta.yaml b/packages/annsel/meta.yaml index 6b3a3a00..caec5064 100644 --- a/packages/annsel/meta.yaml +++ b/packages/annsel/meta.yaml @@ -8,6 +8,7 @@ tutorials_home: https://annsel.readthedocs.io/page/notebooks/all_of_annsel.html install: pypi: annsel license: MIT +language: Python version: v0.0.8 contact: - srivarra diff --git a/packages/benGRN/meta.yaml b/packages/benGRN/meta.yaml index 977204e1..2ad561b9 100644 --- a/packages/benGRN/meta.yaml +++ b/packages/benGRN/meta.yaml @@ -14,6 +14,7 @@ tags: - gene regulatory networks - benchmarking license: MIT +language: Python version: v1.2.1 contact: - jkobject diff --git a/packages/bento-tools/meta.yaml b/packages/bento-tools/meta.yaml index baf6ac7b..fd5ecd5c 100644 --- a/packages/bento-tools/meta.yaml +++ b/packages/bento-tools/meta.yaml @@ -13,6 +13,7 @@ tags: - spatial transcriptomics - segmentation license: BSD-2-Clause +language: Python version: v1.0.1 contact: - ckmah diff --git a/packages/biolord/meta.yaml b/packages/biolord/meta.yaml index 07127a77..eec081a6 100644 --- a/packages/biolord/meta.yaml +++ b/packages/biolord/meta.yaml @@ -12,6 +12,7 @@ tags: - perturbation - deep learning license: BSD-3-Clause +language: Python version: v0.0.1 contact: - zoepiran diff --git a/packages/cell2location/meta.yaml b/packages/cell2location/meta.yaml index 0207feec..e4d55d8f 100644 --- a/packages/cell2location/meta.yaml +++ b/packages/cell2location/meta.yaml @@ -18,6 +18,7 @@ tags: - deconvolution - probabilistic modeling license: Apache-2.0 +language: Python version: v0.1 contact: - vitkl diff --git a/packages/cellxgene/meta.yaml b/packages/cellxgene/meta.yaml index 4b462aa3..aa2822fe 100644 --- a/packages/cellxgene/meta.yaml +++ b/packages/cellxgene/meta.yaml @@ -13,6 +13,7 @@ tags: - cell-type annotation - visualization license: MIT +language: Python version: 1.1.1 contact: - csweaver diff --git a/packages/clone2vec/meta.yaml b/packages/clone2vec/meta.yaml index 7d87ef79..475de88f 100644 --- a/packages/clone2vec/meta.yaml +++ b/packages/clone2vec/meta.yaml @@ -10,6 +10,7 @@ primary_category: scRNA-seq tags: - lineage tracing license: MIT +language: Python publications: - 10.1101/2024.11.15.623687 version: v0.1.0 diff --git a/packages/cookiecutter-scverse/meta.yaml b/packages/cookiecutter-scverse/meta.yaml index c6f3f619..e99519f5 100644 --- a/packages/cookiecutter-scverse/meta.yaml +++ b/packages/cookiecutter-scverse/meta.yaml @@ -7,6 +7,7 @@ primary_category: Infrastructure tags: - documentation license: BSD-3-Clause +language: Python version: 0.6.0 contact: - grst diff --git a/packages/dandelion/meta.yaml b/packages/dandelion/meta.yaml index 56f8ba6b..1c7b85c8 100644 --- a/packages/dandelion/meta.yaml +++ b/packages/dandelion/meta.yaml @@ -16,6 +16,7 @@ primary_category: Adaptive immune cell receptor tags: - immune receptor license: AGPL-3.0-or-later +language: Python version: v0.3.0 contact: - zktuong diff --git a/packages/decoupler/meta.yaml b/packages/decoupler/meta.yaml index a43e0890..544d5a22 100644 --- a/packages/decoupler/meta.yaml +++ b/packages/decoupler/meta.yaml @@ -14,6 +14,7 @@ primary_category: scRNA-seq tags: - functional analysis license: BSD-3-Clause +language: Python version: 2.1.1 contact: - PauBadiaM diff --git a/packages/delnx/meta.yaml b/packages/delnx/meta.yaml index 8d545768..0c156abd 100644 --- a/packages/delnx/meta.yaml +++ b/packages/delnx/meta.yaml @@ -10,6 +10,7 @@ primary_category: scRNA-seq tags: - differential expression license: MIT +language: Python version: v0.2.3 contact: - joschif diff --git a/packages/dvp-io/meta.yaml b/packages/dvp-io/meta.yaml index fa838436..a8501b4c 100644 --- a/packages/dvp-io/meta.yaml +++ b/packages/dvp-io/meta.yaml @@ -12,6 +12,7 @@ tags: - proteomics - file formats license: Apache-2.0 +language: Python version: 0.5.1 contact: - lucas-diedrich diff --git a/packages/dynamo-release/meta.yaml b/packages/dynamo-release/meta.yaml index 50eb7042..f51b449b 100644 --- a/packages/dynamo-release/meta.yaml +++ b/packages/dynamo-release/meta.yaml @@ -16,6 +16,7 @@ tags: - trajectory inference - RNA velocity license: BSD-3-Clause +language: Python version: v1.1.0 contact: - Xiaojieqiu diff --git a/packages/ecosystem-packages/meta.yaml b/packages/ecosystem-packages/meta.yaml index 56c3d4a1..7433e423 100644 --- a/packages/ecosystem-packages/meta.yaml +++ b/packages/ecosystem-packages/meta.yaml @@ -7,6 +7,7 @@ primary_category: Infrastructure tags: - documentation license: BSD-3-Clause +language: Python contact: - grst - flying-sheep diff --git a/packages/epiScanpy/meta.yaml b/packages/epiScanpy/meta.yaml index 009e6b96..aa17af0c 100644 --- a/packages/epiScanpy/meta.yaml +++ b/packages/epiScanpy/meta.yaml @@ -13,6 +13,7 @@ primary_category: Epigenomics tags: - epigenomics license: BSD-3-Clause +language: Python version: v0.3.2 contact: - DaneseAnna diff --git a/packages/eschr/meta.yaml b/packages/eschr/meta.yaml index 1d6215e4..d85a7097 100644 --- a/packages/eschr/meta.yaml +++ b/packages/eschr/meta.yaml @@ -14,6 +14,7 @@ tags: - clustering - probabilistic modeling license: "MIT" +language: Python version: v1.0.1 contact: - smgoggin10 diff --git a/packages/favapy/meta.yaml b/packages/favapy/meta.yaml index a66ecddc..1a623f07 100644 --- a/packages/favapy/meta.yaml +++ b/packages/favapy/meta.yaml @@ -16,6 +16,7 @@ tags: - dimensionality reduction - deep learning license: MIT +language: Python version: v0.3.9.4 contact: - mikelkou diff --git a/packages/flashdeconv/meta.yaml b/packages/flashdeconv/meta.yaml index 62d8476d..52772798 100644 --- a/packages/flashdeconv/meta.yaml +++ b/packages/flashdeconv/meta.yaml @@ -18,6 +18,7 @@ tags: - cell-type annotation - deconvolution license: BSD-3-Clause +language: Python version: v0.1 contact: - cafferychen777 diff --git a/packages/flowsom/meta.yaml b/packages/flowsom/meta.yaml index 25f08647..0306a0e3 100644 --- a/packages/flowsom/meta.yaml +++ b/packages/flowsom/meta.yaml @@ -19,6 +19,7 @@ tags: - flow cytometry - clustering license: GPL-3.0-only +language: Python version: v0.0.1 contact: - artuurC diff --git a/packages/governance/meta.yaml b/packages/governance/meta.yaml index 57dc3f56..e9440ad5 100644 --- a/packages/governance/meta.yaml +++ b/packages/governance/meta.yaml @@ -7,6 +7,7 @@ primary_category: Infrastructure tags: - documentation license: BSD-3-Clause +language: Python contact: - Zethson - gtca diff --git a/packages/grassp/meta.yaml b/packages/grassp/meta.yaml index 3e90db77..24046e79 100644 --- a/packages/grassp/meta.yaml +++ b/packages/grassp/meta.yaml @@ -14,6 +14,7 @@ tags: - spatial proteomics - proteomics license: BSD-3-Clause +language: Python version: v0.1.0 contact: - mffrank diff --git a/packages/gssnng/meta.yaml b/packages/gssnng/meta.yaml index 2e58e568..817e5f74 100644 --- a/packages/gssnng/meta.yaml +++ b/packages/gssnng/meta.yaml @@ -14,6 +14,7 @@ tags: - preprocessing - functional analysis license: MIT +language: Python version: v0.4.2 contact: - gibbsdavidl diff --git a/packages/hotspot/meta.yaml b/packages/hotspot/meta.yaml index e0974c5b..5dc156ee 100644 --- a/packages/hotspot/meta.yaml +++ b/packages/hotspot/meta.yaml @@ -13,6 +13,7 @@ tags: - functional analysis - gene regulatory networks license: BSD-3-Clause +language: Python version: v1.1.1 contact: - deto diff --git a/packages/illico/meta.yaml b/packages/illico/meta.yaml index 844797d4..0f6aa722 100644 --- a/packages/illico/meta.yaml +++ b/packages/illico/meta.yaml @@ -12,6 +12,7 @@ tags: - scRNA-seq - differential expression license: Apache-2.0 +language: Python version: 0.1.1 contact: - remydubois diff --git a/packages/infercnvpy/meta.yaml b/packages/infercnvpy/meta.yaml index 809eb0a6..472b0593 100644 --- a/packages/infercnvpy/meta.yaml +++ b/packages/infercnvpy/meta.yaml @@ -10,6 +10,7 @@ primary_category: scRNA-seq tags: - copy number variation license: BSD-3-Clause +language: Python version: v0.3.0 contact: - grst diff --git a/packages/integration-testing/meta.yaml b/packages/integration-testing/meta.yaml index 68f4b57c..03a9c579 100644 --- a/packages/integration-testing/meta.yaml +++ b/packages/integration-testing/meta.yaml @@ -7,6 +7,7 @@ primary_category: Infrastructure tags: - benchmarking license: MIT +language: Python contact: - ilan-gold - flying-sheep diff --git a/packages/kompot/meta.yaml b/packages/kompot/meta.yaml index a75ccd2c..b68a7dae 100644 --- a/packages/kompot/meta.yaml +++ b/packages/kompot/meta.yaml @@ -20,6 +20,7 @@ tags: - compositional analysis - probabilistic modeling license: GPL-3.0-or-later +language: Python version: v0.6.1 contact: - katosh diff --git a/packages/liana/meta.yaml b/packages/liana/meta.yaml index f9be4f50..1e508641 100644 --- a/packages/liana/meta.yaml +++ b/packages/liana/meta.yaml @@ -11,6 +11,7 @@ tags: - spatial transcriptomics - cell-cell communication license: GPL-3.0-only +language: Python version: v1.0.0a1 contact: - dbdimitrov diff --git a/packages/maxspin/meta.yaml b/packages/maxspin/meta.yaml index 973fc66d..d2efbb32 100644 --- a/packages/maxspin/meta.yaml +++ b/packages/maxspin/meta.yaml @@ -12,6 +12,7 @@ primary_category: Spatial tags: - spatially variable genes license: MIT +language: Python version: v0.1.1 contact: - dcjones diff --git a/packages/moscot/meta.yaml b/packages/moscot/meta.yaml index 8604b1c5..c908f351 100644 --- a/packages/moscot/meta.yaml +++ b/packages/moscot/meta.yaml @@ -14,6 +14,7 @@ tags: - trajectory inference - optimal transport license: BSD-3-Clause +language: Python version: v0.4.0 contact: - MUCDK diff --git a/packages/mudata/meta.yaml b/packages/mudata/meta.yaml index eb58af5c..88f441c4 100644 --- a/packages/mudata/meta.yaml +++ b/packages/mudata/meta.yaml @@ -16,6 +16,7 @@ tags: - multimodal - data structures license: BSD-3-Clause +language: Python version: 0.3.2 contact: - gtca diff --git a/packages/muon/meta.yaml b/packages/muon/meta.yaml index 63f890e2..14352600 100644 --- a/packages/muon/meta.yaml +++ b/packages/muon/meta.yaml @@ -15,6 +15,7 @@ tags: - multimodal - data integration license: BSD-3-Clause +language: Python version: 0.1.7 contact: - gtca diff --git a/packages/nichepca/meta.yaml b/packages/nichepca/meta.yaml index 7c887a93..3cdd8228 100644 --- a/packages/nichepca/meta.yaml +++ b/packages/nichepca/meta.yaml @@ -11,6 +11,7 @@ tags: - spatial transcriptomics - clustering license: MIT +language: Python version: v0.0.3 contact: - dschaub95 diff --git a/packages/novae/meta.yaml b/packages/novae/meta.yaml index b3f5362c..45723631 100644 --- a/packages/novae/meta.yaml +++ b/packages/novae/meta.yaml @@ -13,6 +13,7 @@ tags: - spatial transcriptomics - deep learning license: BSD-3-Clause +language: Python version: v0.2.1 contact: - quentinblampey diff --git a/packages/omicverse/meta.yaml b/packages/omicverse/meta.yaml index e769387b..27869386 100644 --- a/packages/omicverse/meta.yaml +++ b/packages/omicverse/meta.yaml @@ -14,6 +14,7 @@ tags: - bulk RNA-seq - multimodal license: GPL-3.0-only +language: Python version: v1.4.12 contact: - Starlitnightly diff --git a/packages/palantir/meta.yaml b/packages/palantir/meta.yaml index f1a60279..0673bcd9 100644 --- a/packages/palantir/meta.yaml +++ b/packages/palantir/meta.yaml @@ -19,6 +19,7 @@ tags: - dimensionality reduction - trajectory inference license: GPL-2.0-or-later +language: Python version: v1.3.3 contact: - ManuSetty diff --git a/packages/panpipes/meta.yaml b/packages/panpipes/meta.yaml index a99f224f..9509d267 100644 --- a/packages/panpipes/meta.yaml +++ b/packages/panpipes/meta.yaml @@ -14,6 +14,7 @@ tags: - multimodal - pipeline license: BSD-3-Clause +language: Python version: v0.5.0 contact: - bio-la diff --git a/packages/pcdl/meta.yaml b/packages/pcdl/meta.yaml index cfec76ba..c666cc1e 100644 --- a/packages/pcdl/meta.yaml +++ b/packages/pcdl/meta.yaml @@ -6,6 +6,7 @@ tutorials_home: https://github.com/elmbeech/physicelldataloader/blob/master/man/ install: pypi: pcdl license: BSD-3-Clause +language: Python primary_category: Infrastructure tags: - file formats diff --git a/packages/pegasus/meta.yaml b/packages/pegasus/meta.yaml index 6a95d20e..59152873 100644 --- a/packages/pegasus/meta.yaml +++ b/packages/pegasus/meta.yaml @@ -15,6 +15,7 @@ tags: - cell-type annotation - clustering license: BSD-3-Clause +language: Python version: v1.7.1 contact: - yihming diff --git a/packages/pertpy/meta.yaml b/packages/pertpy/meta.yaml index cf9adf20..e0551f8d 100644 --- a/packages/pertpy/meta.yaml +++ b/packages/pertpy/meta.yaml @@ -16,6 +16,7 @@ tags: - differential expression - perturbation license: MIT +language: Python version: 1.0.3 contact: - Zethson diff --git a/packages/popV/meta.yaml b/packages/popV/meta.yaml index 254b2f08..6332ebee 100644 --- a/packages/popV/meta.yaml +++ b/packages/popV/meta.yaml @@ -10,6 +10,7 @@ tags: - data integration - cell-type annotation license: MIT +language: Python version: v0.5.2 contact: - canergen diff --git a/packages/pyCrossTalkeR/meta.yaml b/packages/pyCrossTalkeR/meta.yaml index 47311ec3..43d1f749 100644 --- a/packages/pyCrossTalkeR/meta.yaml +++ b/packages/pyCrossTalkeR/meta.yaml @@ -11,6 +11,7 @@ tags: - scRNA-seq - cell-cell communication license: MIT +language: Python version: v2.1.0 contact: - jsnagai diff --git a/packages/pyLemur/meta.yaml b/packages/pyLemur/meta.yaml index c1752227..be09f9db 100644 --- a/packages/pyLemur/meta.yaml +++ b/packages/pyLemur/meta.yaml @@ -12,6 +12,7 @@ primary_category: scRNA-seq tags: - differential expression license: MIT +language: Python version: v0.1.0 contact: - const-ae diff --git a/packages/pySCENIC/meta.yaml b/packages/pySCENIC/meta.yaml index 44fa0e4e..db66b4cc 100644 --- a/packages/pySCENIC/meta.yaml +++ b/packages/pySCENIC/meta.yaml @@ -18,6 +18,7 @@ tags: - gene regulatory networks - clustering license: GPL-3.0-only +language: Python version: v0.12.0 contact: - bramvds diff --git a/packages/pyUCell/meta.yaml b/packages/pyUCell/meta.yaml index ef729123..bbf3f9e5 100644 --- a/packages/pyUCell/meta.yaml +++ b/packages/pyUCell/meta.yaml @@ -17,6 +17,7 @@ primary_category: scRNA-seq tags: - functional analysis license: MIT +language: Python version: v0.3.0 contact: - mass-a diff --git a/packages/pycea/meta.yaml b/packages/pycea/meta.yaml index 3b0f253d..72189d96 100644 --- a/packages/pycea/meta.yaml +++ b/packages/pycea/meta.yaml @@ -11,6 +11,7 @@ tags: - lineage tracing - data structures license: BSD-3-Clause +language: Python version: v0.1.0 contact: - colganwi diff --git a/packages/pychromVAR/meta.yaml b/packages/pychromVAR/meta.yaml index 1f958372..d3e8ec6b 100644 --- a/packages/pychromVAR/meta.yaml +++ b/packages/pychromVAR/meta.yaml @@ -11,6 +11,7 @@ tags: - ATAC-seq - gene regulatory networks license: MIT +language: Python version: v0.0.3 contact: - lzj1769 diff --git a/packages/pytximport/meta.yaml b/packages/pytximport/meta.yaml index c563c30b..5ad094d6 100644 --- a/packages/pytximport/meta.yaml +++ b/packages/pytximport/meta.yaml @@ -12,6 +12,7 @@ tags: - differential expression - file formats license: GPL-3.0-only +language: Python version: v0.2.0 contact: - maltekuehl diff --git a/packages/rapids-singlecell/meta.yaml b/packages/rapids-singlecell/meta.yaml index d752bca2..ea001b80 100644 --- a/packages/rapids-singlecell/meta.yaml +++ b/packages/rapids-singlecell/meta.yaml @@ -13,6 +13,7 @@ tags: - clustering - GPU acceleration license: MIT +language: Python version: 0.13.3 contact: - Intron7 diff --git a/packages/scCellFie/meta.yaml b/packages/scCellFie/meta.yaml index 64e7c5a0..c0119c40 100644 --- a/packages/scCellFie/meta.yaml +++ b/packages/scCellFie/meta.yaml @@ -12,6 +12,7 @@ tags: - functional analysis - cell-cell communication license: MIT +language: Python version: v0.4.5 contact: - earmingol diff --git a/packages/scDataLoader/meta.yaml b/packages/scDataLoader/meta.yaml index ee96aa01..3219c4bf 100644 --- a/packages/scDataLoader/meta.yaml +++ b/packages/scDataLoader/meta.yaml @@ -16,6 +16,7 @@ tags: - deep learning - file formats license: MIT +language: Python version: v1.2.2 contact: - jkobject diff --git a/packages/scFates/meta.yaml b/packages/scFates/meta.yaml index b0a14b5d..6e42588f 100644 --- a/packages/scFates/meta.yaml +++ b/packages/scFates/meta.yaml @@ -13,6 +13,7 @@ tags: - trajectory inference - pseudotime license: BSD-3-Clause +language: Python version: v1.0.0 contact: - LouisFaure diff --git a/packages/scGen/meta.yaml b/packages/scGen/meta.yaml index e5c54361..bbd260e9 100644 --- a/packages/scGen/meta.yaml +++ b/packages/scGen/meta.yaml @@ -13,6 +13,7 @@ primary_category: scRNA-seq tags: - perturbation license: GPL-3.0-only +language: Python version: v2.1.0 contact: - M0hammadL diff --git a/packages/scPRINT-2/meta.yaml b/packages/scPRINT-2/meta.yaml index 422a54e8..aac011d3 100644 --- a/packages/scPRINT-2/meta.yaml +++ b/packages/scPRINT-2/meta.yaml @@ -19,6 +19,7 @@ tags: - deep learning - foundation model license: GPL-3.0-or-later +language: Python version: v1.0.0 contact: - jkobject diff --git a/packages/scPRINT/meta.yaml b/packages/scPRINT/meta.yaml index 7920a12b..873a2121 100644 --- a/packages/scPRINT/meta.yaml +++ b/packages/scPRINT/meta.yaml @@ -17,6 +17,7 @@ tags: - deep learning - foundation model license: MIT +language: Python version: v1.6.2 contact: - jkobject diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml index a5d779d4..010a757a 100644 --- a/packages/scXpand/meta.yaml +++ b/packages/scXpand/meta.yaml @@ -15,6 +15,7 @@ tags: - immune receptor - deep learning license: MIT +language: Python version: v0.4.3 contact: - ronamit diff --git a/packages/scanpro/meta.yaml b/packages/scanpro/meta.yaml index b6db01fb..30b08631 100644 --- a/packages/scanpro/meta.yaml +++ b/packages/scanpro/meta.yaml @@ -12,6 +12,7 @@ tags: - multimodal - compositional analysis license: MIT +language: Python version: 0.2.0 contact: - yalayoubi diff --git a/packages/scanpy/meta.yaml b/packages/scanpy/meta.yaml index 4d415418..25f77091 100644 --- a/packages/scanpy/meta.yaml +++ b/packages/scanpy/meta.yaml @@ -19,6 +19,7 @@ tags: - clustering - visualization license: BSD-3-Clause +language: Python version: 1.11.5 contact: - flying-sheep diff --git a/packages/schist/meta.yaml b/packages/schist/meta.yaml index e2a07b76..93c63d86 100644 --- a/packages/schist/meta.yaml +++ b/packages/schist/meta.yaml @@ -6,6 +6,7 @@ tutorials_home: https://schist.readthedocs.io/page/tutorials.html install: conda: conda-forge::schist license: BSD-3-Clause +language: Python primary_category: scRNA-seq tags: - clustering diff --git a/packages/scib-rapids/meta.yaml b/packages/scib-rapids/meta.yaml index 5d7511ac..e042ede7 100644 --- a/packages/scib-rapids/meta.yaml +++ b/packages/scib-rapids/meta.yaml @@ -12,6 +12,7 @@ tags: - benchmarking - GPU acceleration license: BSD-3-Clause +language: Python version: 0.1.0 contact: - maarten-devries diff --git a/packages/scib/meta.yaml b/packages/scib/meta.yaml index c5ea990a..45b29bfe 100644 --- a/packages/scib/meta.yaml +++ b/packages/scib/meta.yaml @@ -12,6 +12,7 @@ tags: - data integration - benchmarking license: MIT +language: Python version: v1.0.5 contact: - mumichae diff --git a/packages/scirpy/meta.yaml b/packages/scirpy/meta.yaml index d6a0f30e..4ce1ac78 100644 --- a/packages/scirpy/meta.yaml +++ b/packages/scirpy/meta.yaml @@ -15,6 +15,7 @@ primary_category: Adaptive immune cell receptor tags: - immune receptor license: BSD-3-Clause +language: Python version: 0.22.3 contact: - grst diff --git a/packages/scmcp/meta.yaml b/packages/scmcp/meta.yaml index 42db75b1..9b8326dc 100644 --- a/packages/scmcp/meta.yaml +++ b/packages/scmcp/meta.yaml @@ -8,6 +8,7 @@ primary_category: Infrastructure tags: - large language models license: BSD-3-Clause +language: Python version: v0.2.2 contact: - huangsh diff --git a/packages/sctriangulate/meta.yaml b/packages/sctriangulate/meta.yaml index 10611596..75a0ed34 100644 --- a/packages/sctriangulate/meta.yaml +++ b/packages/sctriangulate/meta.yaml @@ -12,6 +12,7 @@ primary_category: scRNA-seq tags: - clustering license: MIT +language: Python version: v0.12.0 contact: - frankligy diff --git a/packages/scvelo/meta.yaml b/packages/scvelo/meta.yaml index eba2ea52..b5fa2f63 100644 --- a/packages/scvelo/meta.yaml +++ b/packages/scvelo/meta.yaml @@ -11,6 +11,7 @@ primary_category: scRNA-seq tags: - RNA velocity license: BSD-3-Clause +language: Python version: v0.2.5 contact: - WeilerP diff --git a/packages/scverse-tutorials/meta.yaml b/packages/scverse-tutorials/meta.yaml index 7bcd9c98..1439e513 100644 --- a/packages/scverse-tutorials/meta.yaml +++ b/packages/scverse-tutorials/meta.yaml @@ -8,6 +8,7 @@ primary_category: Infrastructure tags: - documentation license: BSD-3-Clause +language: Python contact: - grst - flying-sheep diff --git a/packages/scverse.github.io/meta.yaml b/packages/scverse.github.io/meta.yaml index 56cd38ac..ee575ee5 100644 --- a/packages/scverse.github.io/meta.yaml +++ b/packages/scverse.github.io/meta.yaml @@ -7,6 +7,7 @@ primary_category: Infrastructure tags: - documentation license: BSD-3-Clause +language: Python authors: - gtca category: core-infrastructure diff --git a/packages/scvi-tools/meta.yaml b/packages/scvi-tools/meta.yaml index e733b18f..bf71bee9 100644 --- a/packages/scvi-tools/meta.yaml +++ b/packages/scvi-tools/meta.yaml @@ -37,6 +37,7 @@ tags: - deep learning - probabilistic modeling license: BSD-3-Clause +language: Python version: 1.4.0.post1 contact: - ori-kron-wis diff --git a/packages/scxmatch/meta.yaml b/packages/scxmatch/meta.yaml index 981b94b1..6a5f24f1 100644 --- a/packages/scxmatch/meta.yaml +++ b/packages/scxmatch/meta.yaml @@ -15,6 +15,7 @@ tags: - perturbation - probabilistic modeling license: MIT +language: Python version: v0.1.0 contact: - annmoel diff --git a/packages/scyan/meta.yaml b/packages/scyan/meta.yaml index 85c6220f..6ded235a 100644 --- a/packages/scyan/meta.yaml +++ b/packages/scyan/meta.yaml @@ -16,6 +16,7 @@ tags: - data integration - cell-type annotation license: BSD-3-Clause +language: Python version: v1.5.0 contact: - quentinblampey diff --git a/packages/sift-sc/meta.yaml b/packages/sift-sc/meta.yaml index 849296de..8619805c 100644 --- a/packages/sift-sc/meta.yaml +++ b/packages/sift-sc/meta.yaml @@ -11,6 +11,7 @@ primary_category: scRNA-seq tags: - preprocessing license: BSD-3-Clause +language: Python version: v0.1.0 contact: - zoepiran diff --git a/packages/sincei/meta.yaml b/packages/sincei/meta.yaml index d359f20e..c663998e 100644 --- a/packages/sincei/meta.yaml +++ b/packages/sincei/meta.yaml @@ -21,6 +21,7 @@ tags: - visualization - file formats license: MIT +language: Python version: v0.5.1 authors: - vivekbhr diff --git a/packages/sobolev-alignment/meta.yaml b/packages/sobolev-alignment/meta.yaml index 7bf0c2ed..f8462413 100644 --- a/packages/sobolev-alignment/meta.yaml +++ b/packages/sobolev-alignment/meta.yaml @@ -13,6 +13,7 @@ tags: - deep learning - probabilistic modeling license: MIT +language: Python version: 1.0.0 contact: - saroudant diff --git a/packages/sopa/meta.yaml b/packages/sopa/meta.yaml index 5bfa88bd..43ff5c6b 100644 --- a/packages/sopa/meta.yaml +++ b/packages/sopa/meta.yaml @@ -15,6 +15,7 @@ tags: - imaging - pipeline license: BSD-3-Clause +language: Python version: v1.0.0 contact: - quentinblampey diff --git a/packages/spatial-eggplant/meta.yaml b/packages/spatial-eggplant/meta.yaml index a691c61a..e9ed92ed 100644 --- a/packages/spatial-eggplant/meta.yaml +++ b/packages/spatial-eggplant/meta.yaml @@ -13,6 +13,7 @@ tags: - spatial transcriptomics - data integration license: MIT +language: Python version: v0.2.3 contact: - almaan diff --git a/packages/spatialdata/meta.yaml b/packages/spatialdata/meta.yaml index c6d218e3..85bd1b05 100644 --- a/packages/spatialdata/meta.yaml +++ b/packages/spatialdata/meta.yaml @@ -16,6 +16,7 @@ tags: - data structures - file formats license: BSD-3-Clause +language: Python version: 0.5.0 contact: - LucaMarconato diff --git a/packages/spatialproteomics/meta.yaml b/packages/spatialproteomics/meta.yaml index 8a160ecc..d87a35ca 100644 --- a/packages/spatialproteomics/meta.yaml +++ b/packages/spatialproteomics/meta.yaml @@ -15,6 +15,7 @@ tags: - imaging - pipeline license: MIT +language: Python version: v0.7.0 contact: - MeyerBender diff --git a/packages/spatiomic/meta.yaml b/packages/spatiomic/meta.yaml index 604fbeb4..afb8c6a7 100644 --- a/packages/spatiomic/meta.yaml +++ b/packages/spatiomic/meta.yaml @@ -13,6 +13,7 @@ tags: - imaging - segmentation license: GPL-3.0-only +language: Python version: v0.5.0 contact: - maltekuehl diff --git a/packages/squidpy/meta.yaml b/packages/squidpy/meta.yaml index 9817c493..0dc75aa0 100644 --- a/packages/squidpy/meta.yaml +++ b/packages/squidpy/meta.yaml @@ -17,6 +17,7 @@ tags: - spatial transcriptomics - imaging license: BSD-3-Clause +language: Python version: 1.6.5 contact: - giovp diff --git a/packages/stats/meta.yaml b/packages/stats/meta.yaml index 8ee439f6..5ad217ab 100644 --- a/packages/stats/meta.yaml +++ b/packages/stats/meta.yaml @@ -7,6 +7,7 @@ primary_category: Infrastructure tags: - benchmarking license: MIT +language: Python authors: - maltekuehl - grst diff --git a/packages/symphonypy/meta.yaml b/packages/symphonypy/meta.yaml index 146629a2..5dbd9211 100644 --- a/packages/symphonypy/meta.yaml +++ b/packages/symphonypy/meta.yaml @@ -10,6 +10,7 @@ primary_category: scRNA-seq tags: - cell-type annotation license: GPL-3.0-only +language: Python version: v0.2.1 contact: - serjisa diff --git a/packages/tangram/meta.yaml b/packages/tangram/meta.yaml index 30c806e3..b883d09a 100644 --- a/packages/tangram/meta.yaml +++ b/packages/tangram/meta.yaml @@ -13,6 +13,7 @@ tags: - spatial transcriptomics - deconvolution license: BSD-3-Clause +language: Python version: v1.0.3 contact: - ziqlu0722 diff --git a/packages/tau-community-detection/meta.yaml b/packages/tau-community-detection/meta.yaml index 1241104f..4ba4b872 100644 --- a/packages/tau-community-detection/meta.yaml +++ b/packages/tau-community-detection/meta.yaml @@ -9,6 +9,7 @@ documentation_home: https://github.com/HillelCharbit/TAU#readme install: pypi: tau-community-detection license: MIT +language: Python primary_category: scRNA-seq tags: - clustering diff --git a/packages/vitessce/meta.yaml b/packages/vitessce/meta.yaml index 322ee346..a5f6a7ab 100644 --- a/packages/vitessce/meta.yaml +++ b/packages/vitessce/meta.yaml @@ -16,6 +16,7 @@ tags: - multimodal - visualization license: MIT +language: Python version: v3.5.7 contact: - keller-mark diff --git a/packages/wsidata/meta.yaml b/packages/wsidata/meta.yaml index 6deda37c..cd3f43b4 100644 --- a/packages/wsidata/meta.yaml +++ b/packages/wsidata/meta.yaml @@ -11,6 +11,7 @@ tags: - data structures - file formats license: MIT +language: Python version: v0.3.0 contact: - Mr-Milk diff --git a/scripts/src/ecosystem_scripts/schema.json b/scripts/src/ecosystem_scripts/schema.json index 87bab1ea..a912237c 100644 --- a/scripts/src/ecosystem_scripts/schema.json +++ b/scripts/src/ecosystem_scripts/schema.json @@ -260,9 +260,8 @@ "uniqueItems": true }, "language": { - "description": "Language a user writes code in when using the package. Assumed to be Python when omitted.", + "description": "Language a user writes code in when using the package.", "type": "string", - "default": "Python", "enum": ["Python", "R", "Julia", "Rust"] }, "publications": { @@ -315,6 +314,7 @@ "license", "tags", "primary_category", + "language", "category" ], "if": { From 861685d3ec4201875d7902d4d2799b2276dd763f Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Thu, 13 Aug 2026 13:50:43 -0700 Subject: [PATCH 6/6] Update README.md Co-authored-by: Gregor Sturm --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 0ab78e83..5e87730e 100644 --- a/README.md +++ b/README.md @@ -80,7 +80,6 @@ How does the package use scverse data structures (please describe in a few sente - [ ] Continuous integration (CI) automatically executes these tests on each push or pull request [^2] - [ ] The package provides API documentation via a website or README[^3] - [ ] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions) -- [ ] `primary_category` and `tags` are set from the controlled vocabulary documented above - [ ] I am an author or maintainer of the tool and agree on listing the package on the scverse website - [ ] I agree to abide by the [scverse code of conduct](https://scverse.org/about/code_of_conduct/) on all scverse communication channels