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.

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.

lobster-ai

The self-evolving agentic framework for bioinformatics

riptide

Reaction Inclusion by Parsimony and Transcript Distribution (RIPTiDe)

cirrocumulus

Bring your single-cell data to life

rnalysis

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

starfish

starfish: unified pipelines for image-based transcriptomics

hide-deconv

HIDE-Deconv: Interactive command line tool and python package for hierarchical cell type deconvolution and analysis of bulk RNA-seq data.

lobster-ai-tui

The self-evolving agentic framework for bioinformatics

cellxgene

An interactive explorer for single-cell transcriptomics data

trisicell

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

scgen

Single cell perturbation prediction

drvi-py

Unsupervised Deep Disentangled Representation of Single-Cell Omics

cytetype

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

digitalcellsorter

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

scxpand

Pan-cancer detection of T-cell clonal expansion from single-cell RNA sequencing

isoform-dominance

Config-driven, CI-tested pipeline for isoform-usage quantification from bulk RNA-seq (Salmon + paired statistics).

lobster-transcriptomics

The self-evolving agentic framework for bioinformatics

lobster-visualization

The self-evolving agentic framework for bioinformatics