Differential Expression Python Packages

pydeseq2

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

adpbulk

pseudobulking on an AnnData object

rosetta-bioc

Rosetta Stone between R and Python for bio

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

normalisr

Causal inference, differential expression, and co-expression for scRNA-seq

dimet

Differential analysis of targeted Isotope-labeled Metabolomics data

curare

Curare: A Customizable and Reproducible Analysis Pipeline for RNA-Seq Experiments

idea-bio

Integrated Differential Expression and Annotation

pylimma

Python port of R limma for differential expression analysis

manorm

A robust model for quantitative comparison of ChIP-Seq data sets.

degenome

Differential expression across the genome

ncountr

Python pipeline for Nanostring nCounter gene expression analysis — parse, QC, normalize, DE, pathway scoring

tapir-rna

Transcriptiome Analysis in Python Imported from R

scarf-toolkit

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.