satijalab / seurat
R toolkit for single cell genomics
satijalab / seurat
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
saeyslab / nichenetr
NicheNet: predict active ligand-target links between interacting cells
scverse / squidpy
Spatial Single Cell Analysis in Python
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.