Bioinformatics Python Packages

dash

Data Apps & Dashboards for Python. No JavaScript Required.

biopython

Official git repository for Biopython (originally converted from CVS)

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.

biotite

A comprehensive library for computational molecular biology

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

pydeseq2

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

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

edlib

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

pronto

A Python frontend to (Open Biomedical) Ontologies.

eutils

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

cyvcf2

cython + htslib == fast VCF and BCF processing

pyhmmer

Cython bindings and Python interface to HMMER3.

pymzml

pymzML - an interface between Python and mzML Mass spectrometry Files

scikit-bio

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

harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

bioutils

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

pyfamsa

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

mmcif-pdbx

Yet another version of PDBx/mmCIF Python implementation

biocommons-seqrepo

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

pdb2pqr

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