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.

gget

🧬 gget enables efficient querying of genomic reference databases

decoupler

Python package to perform enrichment analysis from omics data.

starfish

starfish: unified pipelines for image-based transcriptomics

brisc

Fast single-cell toolkit

nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

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.

riptide

Reaction Inclusion by Parsimony and Transcript Distribution

cirrocumulus

Bring your single-cell data to life

openomicsbench

Traceable omics benchmarks with multi-method matrices, regression gates, portable bundles and sequence tools.

piaso-tools

PIASO: Precise Integrative Analysis of Single-cell Omics

lobster-ai

The self-evolving agentic framework for bioinformatics

isoform-dominance

Is this functional isoform-class comparison measurable by short reads? Group-level identifiability, quantification and testing from bulk RNA-seq

lobster-ai-tui

The self-evolving agentic framework for bioinformatics

hide-deconv

Hierarchical cell-type deconvolution and analysis of bulk RNA-seq data using single-cell references | Python package and CLI

rnalysis

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

cellxgene

An interactive explorer for single-cell transcriptomics data

digitalcellsorter

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

cytetype

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

trisicell

Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

pymultiomics

Python toolbox for multi-omics data mapping and analysis

scxpand

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