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 / scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
nf-core / rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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
scverse / gget
🧬 gget enables efficient querying of genomic reference databases
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
deeptools / deepTools
Tools to process and analyze deep sequencing data.
scverse / PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
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
aristoteleo / dynamo-release
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
styczynski / bioseqdb
Genomic sequence storage, indexing and alignment inside PostgreSQL: https://bioseqdb.com/
heise3 / ExtremaRank
Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk
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.
97YearsOldProgrammer / flashalign
A fast aligner for long DNA and RNA reads.
windmirrorai / nanomirrors
State-of-the-art bio cell models for inference and training. Minimal, readable, and produciton-ready.