scverse · Zethson · Aug 13, 2026 · Aug 11, 2026 · Aug 11, 2026 · Aug 11, 2026
diff --git a/README.md b/README.md
@@ -20,13 +20,47 @@ 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 `primary_category` and `tags` from the controlled vocabulary below
+
+## Categories, tags and language
+
+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.
+
+- `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.
+
+`language` is the language you write in when using the package: `Python`, `R`, `Julia` or `Rust`.
 
 ## What are the requirements for an ecosystem package?
 
 For a package to become an approved ecosystem package, it must fulfill all mandatory requirements from the checklist below.
 
 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
@@ -47,6 +81,7 @@ How does the package use scverse data structures (please describe in a few sente
 - [ ] 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)
 - [ ] 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
@@ -12,16 +12,15 @@ 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
 license: MIT
+language: Python
 version: v0.3.1
 contact:
   - KalinNonchev

diff --git a/packages/CellAnnotator/meta.yaml b/packages/CellAnnotator/meta.yaml
@@ -5,13 +5,12 @@ 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
 license: MIT
+language: Python
 version: v0.1.3
 contact:
   - Marius1311

diff --git a/packages/CellCharter/meta.yaml b/packages/CellCharter/meta.yaml
@@ -8,12 +8,13 @@ publications:
   - 10.1038/s41588-023-01588-4
 install:
   pypi: cellcharter
+primary_category: Spatial
 tags:
-  - spatial omics
-  - spatial clustering
-  - spatial domains
-  - gaussian mixture model
+  - spatial transcriptomics
+  - 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
@@ -5,12 +5,12 @@ 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
+  - 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
@@ -9,10 +9,13 @@ publications:
   - 10.1101/2020.02.17.947416
 install:
   pypi: celloracle
+primary_category: Epigenomics
 tags:
-  - GRN
-  - TF
+  - epigenomics
+  - 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
@@ -10,12 +10,13 @@ publications:
   - 10.1038/s41592-021-01346-6
 install:
   pypi: cellrank
+primary_category: scRNA-seq
 tags:
-  - ML
-  - cell-fate
-  - rna-velocity
-  - trajectory-generation
+  - trajectory inference
+  - 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
@@ -7,9 +7,12 @@ publications:
   - 10.1038/s41467-020-17281-7
 install:
   pypi: Cell-BLAST
+primary_category: scRNA-seq
 tags:
-  - BLAST
+  - 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
@@ -11,14 +11,12 @@ 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
 license: MIT
+language: Python
 version: v5.0.0
 contact:
   - chapuzzo

diff --git a/packages/Cirrocumulus/meta.yaml b/packages/Cirrocumulus/meta.yaml
@@ -8,9 +8,11 @@ publications:
   - 10.1038/s41592-020-0905-x
 install:
   pypi: cirrocumulus
+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
@@ -5,12 +5,12 @@ 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
+  - visualization
 license: MIT
+language: Python
 version: v0.0.2
 contact:
   - davidrm-bio

diff --git a/packages/DRVI/meta.yaml b/packages/DRVI/meta.yaml
@@ -12,13 +12,14 @@ 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
+  - 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
@@ -9,9 +9,11 @@ publications:
   - 10.1016/j.cels.2019.03.003
 install:
   pypi: doubletdetection
+primary_category: scRNA-seq
 tags:
-  - doublet
+  - quality control
 license: MIT
+language: Python
 version: v4.2
 contact:
   - adamgayoso

diff --git a/packages/GPTBioInsightor/meta.yaml b/packages/GPTBioInsightor/meta.yaml
@@ -6,12 +6,12 @@ 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
+  - 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
@@ -8,13 +8,13 @@ publications:
   - 10.1101/2024.07.29.605556
 install:
   pypi: grnndata
+primary_category: Data structures
 tags:
-  - single cell
-  - RNAseq
-  - gene networks
-  - format
-  - utilities
+  - scRNA-seq
+  - 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
@@ -5,11 +5,14 @@ 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
+  - imaging
+  - preprocessing
+  - 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
@@ -7,13 +7,14 @@ publications:
   - 10.1101/2023.02.02.526825
 install:
   pypi: mowgli
+primary_category: Multimodal
 tags:
-  - single cell
-  - optimal transport
-  - multi omics
+  - multimodal
   - data integration
-  - NMF
+  - 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
@@ -9,9 +9,12 @@ publications:
   - 10.1038/s41587-022-01476-y
 install:
   pypi: multivelo
+primary_category: Epigenomics
 tags:
-  - rna velocity
+  - 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
@@ -6,11 +6,12 @@ publications:
   - 10.1101/2025.02.20.639146
 install:
   pypi: peakqc
+primary_category: Epigenomics
 tags:
-  - single cell
   - 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
@@ -15,14 +15,14 @@ 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
+  - imaging
+  - multimodal
+  - 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
@@ -7,11 +7,10 @@ tutorials_home: https://partipy.readthedocs.io/
 install:
   pypi: partipy
 license: MIT
+language: Python
+primary_category: scRNA-seq
 tags:
-  - "single cell"
-  - "archetypal analysis"
-  - "division of labor"
-  - "representation learning"
+  - dimensionality reduction
 version: v0.0.04
 contact:
   - psl-schaefer