seandavi / awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

scverse / scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

chanzuckerberg / cellxgene

An interactive explorer for single-cell transcriptomics data

windmirrorai / nanomirrors

State-of-the-art bio cell models for inference and training. Minimal, readable, and produciton-ready.

mdozmorov / scRNA-seq_notes

A list of scRNA-seq analysis tools

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

aristoteleo / dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

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.