Tabula Muris 2018 — mouse multi-organ atlas (immune subset re-analysis)

Re-analysis of the publicly available single-cell dataset from:

The Tabula Muris Consortium. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris.
Nature 2018. https://doi.org/10.1038/s41586-018-0590-4
Data: figshare / GEO: GSE109774

Dataset at a glance

• System: Mouse multi-organ reference atlas — immune-cell compartment
• Assay: 10x Genomics + Smart-seq2 scRNA-seq
• Accession / source: figshare / GEO: GSE109774

What this repository does

Preprocesses the immune-cell compartment of the mouse multi-organ atlas into a Seurat object for cross-tissue immune comparisons. See scripts/01_Tabula_Muris_immune_cell_dataset_preprocessing.Rmd.

Repository structure

• scripts/ — analysis pipeline (numbered .Rmd scripts run in order)
• Setup.R / Load_packages.R — environment setup and package loading
• Large data objects are not tracked in Git — download from the source above.

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Part of my NK / T-cell single-cell research programme — see my GitHub profile and dilloncorvino.com.
Author: Dillon Corvino

Environment

Built in R with a Seurat-based single-cell stack — key packages: Seurat, SeuratDisk, scCustomize, dplyr, ggplot2, plus my helper package r-utility-functions.

No pinned renv.lock is committed; the packages listed above are the required dependencies.

Data availability

Raw data is not stored in this repository — download it from the accession / source cited above into the expected data directory before running the pipeline. Processed objects are regenerated by the analysis scripts.