Rna Seq Python Packages

pydeseq2

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

geoparse

Python library to access Gene Expression Omnibus Database (GEO)

gget

🧬 gget enables efficient querying of genomic reference databases

deeptools

Tools to process and analyze deep sequencing data.

helical

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

velocyto

RNA velocity estimation in Python

rnalysis

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

sequana

Sequana: a set of Snakemake NGS pipelines

astk

Alternative Splicing ToolKit

isoquant

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

scdataset

scDataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell Omics

isograph

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

cutseq

✂️ Trim sequencing adapters from NGS data automatically

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.

agfusion

Python package to annotate and visualize gene fusions.

wot

A software package for analyzing snapshots of developmental processes

broad-genepy

A useful module for any CompBio

svist4get

A simple visualisation tool for genomic tracks from sequencing experiments.

cellxgene-gateway

Cellxgene Gateway

pygtftk

The Python GTF toolkit (pygtftk) package: easy handling of GTF files

scprint

single cell foundation model for Gene network inference and more

sequana-rnaseq

RNA-seq, QC and differential analysis pipeline

bintogene

A bin to gene conversion package.