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.

scanpy

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

pyfaidx

Efficient pythonic random access to fasta subsequences

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

mmcif-pdbx

Yet another version of PDBx/mmCIF Python implementation

pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

scikit-bio

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

pydeseq2

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

bioutils

provides common tools and lookup tables used primarily by the hgvs and uta packages

pronto

A Python frontend to (Open Biomedical) Ontologies.

dnaio

Efficiently read and write sequencing data from Python

tskit

Population-scale Ancestral Recombination Graph (ARG) library

biocommons-seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

python-codon-tables

:bar_chart: Codon usage tables in code-friendly format + Python bindings