Rna Seq Python Packages

pydeseq2

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

gget

🧬 gget enables efficient querying of genomic reference databases

geoparse

Python library to access Gene Expression Omnibus Database (GEO)

velocyto

RNA velocity estimation in Python

deeptools

Tools to process and analyze deep sequencing data.

scdataset

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

contig

An agentic bioinformatics analyst: it runs the analysis on your own compute, self-heals failures, verifies the output, and returns a reproducible result.

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

helical

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

openomicsbench

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

cutseq

✂️ Trim sequencing adapters from NGS data automatically

sequana

Sequana: a set of Snakemake NGS pipelines

isoform-dominance

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

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

pylimma

Python port of R limma for differential expression analysis

cytetype

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

discotoolkit

Python version of DISCO toolkit

migec

An UMI-tagged sequencing swiss-knife. Built for amplicon sequencing of immune repertoires, ctDNA and rare mutations, single-cell sequencing.

flashalign

A fast aligner for long DNA and RNA reads.

svist4get

A simple visualisation tool for genomic tracks from sequencing experiments.

bindsight

Expression to Binder: joins cohort RNA-seq target discovery to de novo protein binder design in one reproducible workflow, with PROV-O/RO-Crate provenance from every ranked binder back to the patient samples.

pytximport

Feature-rich Python implementation of the tximport package for gene count estimation.

agfusion

Python package to annotate and visualize gene fusions.