Transcriptomics Python Packages

anndata

Annotated data.

scanpy

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

pydeseq2

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

decoupler

Python package to perform enrichment analysis from omics data.

gget

🧬 gget enables efficient querying of genomic reference databases

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.

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

riptide

Reaction Inclusion by Parsimony and Transcript Distribution

cirrocumulus

Bring your single-cell data to life

lobster-ai

The self-evolving agentic framework for bioinformatics

lobster-ai-tui

The self-evolving agentic framework for bioinformatics

digitalcellsorter

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

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

rnalysis

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

trisicell

No description available

isoquant

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

cellxgene

Web application for exploration of large scale scRNA-seq datasets

isograph

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

starfish

starfish: unified pipelines for image-based transcriptomics

sc-concept

code for scConcept

cytetype

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

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.

scxpand

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

cellxgene-gateway

Cellxgene Gateway