Bioinformatics Tool Python Packages

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures https://hbat-web.abhishek-tiwari.com

bioat

bioat, a python package & command line toolkit for Bioinformatics and data science!

rosettapy

A Python utility for wrapping Rosetta command line tools.

crest-sc

Chunked Rust Engine for Single-cell Transcriptomics

polariseq

Atlas-scale single-cell RNA-seq analysis in Python with a Rust core. Plans memory before reading; runs in memory or out of core.

sjcab-peak2anno-db

Gene-backed peak-to-annotation BED resources for SJ/CAB workflows.

encode-toolkit

MCP server and Claude Code plugin for the ENCODE Project: search, download and analyze ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C and CUT&RUN data with 20 tools, 47 skills and 7 Nextflow pipelines

hide-deconv

Hierarchical cell-type deconvolution and analysis of bulk RNA-seq data using single-cell references | Python package and CLI

finaletoolkit

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

rnalysis

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

tidytcells

Standardise TR/MH/IG data

alphavx

CLI tool that batch-scores VCF variants against AlphaGenome and generates interpretable multi-modal effect reports.

rosetta-finder

A Python utility for wrapping Rosetta command line tools.

binette

A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.

pybio

pybio is a comprehensive Python framework designed to streamline genomics operations. It offers a direct interface to Ensembl genome assemblies and annotations, while also accommodating custom genomes via FASTA/GTF inputs.

gsmap

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

squarna

RNA secondary structure prediction tool

leakhound-ml

Find the data leakage inflating your ML score — duplicates, temporal, target, group, adversarial, and homology (protein/DNA) leaks — and measure the damage. One command, CI-ready.

molforge

A forge for protein workflows. One Python script, every tool in your stack.

pacs-q

PaCS-Q is a Python toolkit designed to assist with Parallel Cascade Selection simulations (PaCS) for studying protein structural transitions in MD and QM/MM MD level.

easyfasta

A lightweight functional Python library for efficient FASTA file parsing and DNA sequence manipulation. No OOP bloat, data only data.

stitchr

Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info

phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

geneview

Genomics data visualization in Python by using matplotlib.