seandavi/awesome-single-cell resource

Health v2 · maintenance only

Adoption not part of the score

3840 stars · 1087 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-29, confidence not recorded

A community-curated awesome list of software packages, tutorials, databases, and data resources for single-cell omics analysis, covering RNA-seq, ATAC-seq, and spatial transcriptomics. It organizes tools by analysis task such as clustering, trajectory inference, batch correction, and cell type annotation.

Use cases

• find software for single-cell RNA-seq analysis
• discover tools for cell clustering and dimensionality reduction
• look up batch-effect removal methods for scRNA-seq
• find trajectory and pseudotime inference packages
• locate spatial transcriptomics analysis tools
• find tutorials and workflows for single-cell data analysis
• discover single-cell databases and web portals

When to choose

• starting a single-cell analysis project and surveying the tool landscape
• comparing available packages for a specific single-cell task like doublet detection or data integration
• building a bioinformatics curriculum or reading list

When to avoid

• you need a ready-to-run analysis pipeline rather than a catalog of options
• you need software itself rather than links to it

Facets

learning-resource · maturity active

data-visualization developer-tools bioinformatics data-science awesome-lists cross-platform single-cell rna-seq atac-seq spatial-transcriptomics genomics curated-list

Member repositories

For agents

markdown · JSON · MCP: product_card(name="seandavi/awesome-single-cell")