theislab/single-cell-tutorial resource

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1589 stars · 489 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

A Jupyter Notebook-based tutorial and case study accompanying the paper 'Current best practices in single-cell RNA-seq analysis: a tutorial' by Luecken and Theis. It demonstrates best-practice workflows for single-cell RNA-seq analysis applied to a mouse intestinal epithelium dataset.

Use cases

• learn single-cell RNA-seq analysis best practices
• reproduce figures from the single-cell RNA-seq tutorial paper
• follow a case study analyzing mouse intestinal epithelium scRNA-seq data
• set up a conda environment for single-cell analysis with Scanpy
• study marker gene detection workflows
• learn preprocessing, clustering, and annotation of scRNA-seq data

When to choose

• you want a guided, paper-backed walkthrough of classic scRNA-seq analysis steps
• you need reproducible notebooks for a published single-cell case study
• you are teaching or learning single-cell transcriptomics fundamentals

When to avoid

• you need the latest single-cell best practices - use the updated sc-best-practices book instead
• you need production-ready software or a maintained analysis pipeline
• you need a tool with an active license or ongoing support

Facets

learning-resource · maturity maintenance

data-science nlp machine-learning data-visualization bioinformatics tutorials python cross-platform single-cell rna-seq scanpy bioinformatics tutorial jupyter-notebook case-study single-cell-rna-seq jupyter

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