Transcriptomics Python Packages | PyPI Stats

anndata

Annotated data.

2M 736 191

scanpy

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

822K 2K 741

pydeseq2

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

477K 748 83

spottedpy

Spatial hotspot analysis

433K 37 0

decoupler

Python package to perform enrichment analysis from omics data.

50K 267 36

gget

🧬 gget enables efficient querying of genomic reference databases

40K 1K 85

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

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

8K 46 10

riptide

Reaction Inclusion by Parsimony and Transcript Distribution

8K 13 7

lobster-ai

The self-evolving agentic framework for bioinformatics

5K 26 6

lobster-ai-tui

The self-evolving agentic framework for bioinformatics

4K 26 6

cirrocumulus

Bring your single-cell data to life

4K 97 18

rnalysis

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

3K 141 13

trisicell

No description available

3K 14 2

digitalcellsorter

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

3K 24 10

cellxgene

An interactive explorer for single-cell transcriptomics data

2K 766 150

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

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

2K 7 1

isoquant

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

2K 222 22

starfish

starfish: unified pipelines for image-based transcriptomics

2K 247 70

scxpand

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

2K 8 4

cytetype

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

2K 127 17

isograph

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

1K 0 0

omnipath-client

Python client for the new OmniPath web APIs

1K 0 0