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scverse
anndata

Annotated data.

2.1M 736 191
scverse
scanpy

Single-cell analysis in Python. Scales to >100M cells.

815K 2K 741
owkin
pydeseq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

532K 748 83
secrierlab
spottedpy

Spatial hotspot analysis

433K 37 0
scverse
decoupler

Python package to perform enrichment analysis from omics data.

49K 267 36
pachterlab
gget

🧬 gget enables efficient querying of genomic reference databases

38K 1K 85
aertslab
pyscenic

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

10K 600 210
microbiomedata
nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

8K 46 10
mjenior
riptide

Reaction Inclusion by Parsimony and Transcript Distribution

8K 13 7
the-omics-os
lobster-ai

The self-evolving agentic framework for bioinformatics

5K 26 6
the-omics-os
lobster-ai-tui

The self-evolving agentic framework for bioinformatics

4K 26 6
lilab-bcb
cirrocumulus

Bring your single-cell data to life

4K 97 18
sdomanskyi
digitalcellsorter

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

3K 24 10
GuyTeichman
rnalysis

Analyze your RNA sequencing data without writing a single line of code

3K 141 13
faridrashidi
trisicell

No description available

3K 14 2
faridrashidi
scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

2K 7 1
chanzuckerberg
cellxgene

An interactive explorer for single-cell transcriptomics data

2K 766 150
spacetx
starfish

starfish: unified pipelines for image-based transcriptomics

2K 247 70
saezlab
omnipath-client

Python client for the new OmniPath web APIs

2K 0 0
dvoelkl
hide-deconv

Repository for ECCB 2026 Poster Submission. Will be made available for reviewing after submission. For earlier access contact Dennis.k.volkl@uib.no

2K 1 0
yizhak-lab-ccg
scxpand

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

2K 8 4
ablab
isoquant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

2K 222 22
NygenAnalytics
cytetype

Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data

2K 127 17
heart-gen
isograph

Python toolkit for discovering isoform-switch and splicing modules from bulk RNA-seq using gene-aware latent network inference.

1K 0 0
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