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.

velocyto

RNA velocity estimation in Python

helical

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

rosetta-bioc

Rosetta Stone between R and Python for bio

sequana

Sequana: a set of Snakemake NGS pipelines

rnalysis

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

scdataset

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

cytetype

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

cutseq

✂️ Trim sequencing adapters from NGS data automatically

isoform-dominance

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

isoquant

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

agfusion

Python package to annotate and visualize gene fusions.

svist4get

A simple visualisation tool for genomic tracks from sequencing experiments.

cello-classify

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

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.

nichenetpy

nichenetpy: the python implementation of the NicheNet method. The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.

scprint

single cell foundation model for Gene network inference and more

broad-genepy

Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python

rna-clique

Compute genetic distance matrices from RNA-seq data.

cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

wot

A software package for analyzing snapshots of developmental processes