Bioinformatics Python Packages

dash

Data Apps & Dashboards for Python. No JavaScript Required.

biopython

Official git repository for Biopython (originally converted from CVS)

biotite

A comprehensive library for computational molecular biology

pyhmmer

Cython bindings and Python interface to HMMER3.

anndata

Annotated data.

pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

pyfaidx

Efficient pythonic random access to fasta subsequences

scanpy

Single-cell analysis in Python. Scales to >100M cells.

spotsweeper

Spatially-aware quality control for spatial transcriptomics

pydeseq2

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

ga4gh-cat-vrs

GA4GH Categorical Variation Representation Python Implementation

ga4gh-va-spec

GA4GH Variation Annotation Python Implementation

ga4gh-vrs

GA4GH Variation Representation Python Implementation

pdbeccdutils

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

cyvcf2

cython + htslib == fast VCF and BCF processing

edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

peppy

Project metadata manager for PEPs in Python

piper

Python toolkit for building restartable pipelines

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

ga4gh

A reference implementation of the GA4GH API

dnaio

Efficiently read and write sequencing data from Python

scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

tskit

Population-scale Ancestral Recombination Graph (ARG) library

galaxy-tool-util

Data intensive science for everyone.