satijalab / seurat
R toolkit for single cell genomics
satijalab / seurat
seandavi / awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
scverse / scanpy
Single-cell analysis in Python. Scales to >100M cells.
scverse / scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
omicverse / omicverse
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
theislab / single-cell-best-practices
https://www.sc-best-practices.org
COMBINE-lab / salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
mdozmorov / scRNA-seq_notes
A list of scRNA-seq analysis tools
chanzuckerberg / cellxgene
An interactive explorer for single-cell transcriptomics data
jinworks / CellChat
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
saeyslab / nichenetr
NicheNet: predict active ligand-target links between interacting cells
immunogenomics / harmony
Fast, sensitive and accurate integration of single-cell data with Harmony
cafferychen777 / mLLMCelltype
Cell type annotation for single-cell RNA-seq using multi-LLM consensus
scverse / squidpy
Spatial Single Cell Analysis in Python
OmicsML / awesome-foundation-model-single-cell-papers
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oncologylab / fp-tools
Command-first ATAC-seq footprinting, motif analysis, and reproducible interactive reports
heise3 / ExtremaRank
Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk
weikaixi / PRISM-GI
PRISM-GI prediction and single-cell analysis code.
sagirimo / BioDSH
The bioinformatics agent desktop for clinicians and wet-lab scientists — built on DeepSeek Harness. One-click installers, a skill store, offline mode.
wrab12 / awesome-spatial-transcriptomics
A curated list of tools, foundation models, datasets and tutorials for spatial transcriptomics and single-cell analysis, ordered the way an analysis goes.
HERRY423 / BioNexus
Scientific reliability layer for AI-assisted biology: evaluates what evidence warrants, caps unsupported claims, audits analytical validity, and prevents silent scientific overreach.