Bioinformatics Tool Python Packages

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures

rosettapy

A Python utility for wrapping Rosetta command line tools.

bioat

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

tidytcells

Standardise TR/MH/IG data

rnalysis

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

finaletoolkit

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

geneview

Genomics data visualization in Python by using matplotlib.

hide-deconv

HIDE-Deconv: Interactive command line tool and python package for hierarchical cell type deconvolution and analysis of bulk RNA-seq data.

molforge

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

easyfasta

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

squarna

RNA secondary structure prediction tool

rosetta-finder

Searching for Rosetta Binaries.

binette

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

biobase

A home for all biological/bioinformatics constants from protein strings to BLOSUM matrices.

encode-toolkit

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

zigo

Zigo: Sex Checking by Zigosity Distributions

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.

gsmap

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

ampidentifier

AMPidentifier: A modular python toolkit for predicting antimicrobial peptides using ensemble machine learning (BR 51 2025 005859-4)

gppy

[G]enomic [P]ositioning with [Py]thon

stitchr

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

ifeatureomegacli

iFeatureOmega is a comprehensive platform for generating, analyzing and visualizing more than 170 representations for biological sequences, 3D structures and ligands. To the best of our knowledge, iFeatureOmega supplies the largest number of feature extraction and analysis approaches for most molecule types compared to other pipelines. Three versions (i.e. iFeatureOmega-Web, iFeatureOmega-GUI and iFeatureOmega-CLI) of iFeatureOmega have been made available to cater to both experienced bioinformaticians and biologists with limited programming expertise. iFeatureOmega also expands its functionality by integrating 15 feature analysis algorithms (including ten cluster algorithms, three dimensionality reduction algorithms and two feature normalization algorithms) and providing nine types of interactive plots for statistical features visualization (including histogram, kernel density plot, heatmap, boxplot, line chart, scatter plot, circular plot, protein three dimensional structure plot and ligand structure plot). iFeatureOmega is an open-source platform for academic purposes. The web server can be accessed through http://ifeature2.erc.monash.edu and the GUI and CLI versions can be download at: https://github.com/Superzchen/iFeatureOmega-GUI and https://github.com/Superzchen/iFeatureOmega-CLI, respectively.

genomap

Genomap converts tabular gene expression data into spatially meaningful images.

phigaro

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