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Transcriptomics Python Packages

Python packages with the GitHub topic transcriptomics. Sorted by relevance, with stars and monthly downloads.
scverse
anndata

Annotated data.

1.7M 740 191
scverse
scanpy

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

828K 2K 742
owkin
pydeseq2

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

117K 750 85
scverse
decoupler

Python package to perform enrichment analysis from omics data.

50K 268 36
pachterlab
gget

🧬 gget enables efficient querying of genomic reference databases

37K 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.

9K 606 211
microbiomedata
nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

7K 46 10
mjenior
riptide

Reaction Inclusion by Parsimony and Transcript Distribution

5K 13 7
lilab-bcb
cirrocumulus

Bring your single-cell data to life

5K 97 17
the-omics-os
lobster-ai

The self-evolving agentic framework for bioinformatics

4K 31 6
the-omics-os
lobster-ai-tui

The self-evolving agentic framework for bioinformatics

4K 31 6
sdomanskyi
digitalcellsorter

Toolkit for analysis and identification of cell types from heterogeneous single cell RNA-seq data

3K 24 10
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

3K 1 0
GuyTeichman
rnalysis

RNAlysis is an analysis software for RNA sequencing data. RNAlysis can help to filter, visualize, explore, analyze, and share your data.

3K 141 13
faridrashidi
trisicell

No description available

3K 14 2
ablab
isoquant

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

3K 224 22
chanzuckerberg
cellxgene

Web application for exploration of large scale scRNA-seq datasets

2K 766 150
heart-gen
isograph

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

2K 0 0
spacetx
starfish

starfish: unified pipelines for image-based transcriptomics

2K 248 71
theislab
sc-concept

code for scConcept

2K 29 4
NygenAnalytics
cytetype

Python client for characterization of clusters from single-cell RNA-seq data.

2K 130 17
UK-SBCoA-EbbertLab
rnapysoforms

A Python package designed for visualizing RNA isoform structures and expression levels by leveraging Plotly for interactive plotting and Polars for efficient data manipulation, enabling the creation of fast-rendering, interactive plots.

1K 9 0
yizhak-lab-ccg
scxpand

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

1K 8 4
Novartis
cellxgene-gateway

Cellxgene Gateway

1K 68 41
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