bioinformatics

Genome assembly evaluation tool

Bioinformatics one liners from Ming Tang

BioMCP: Biomedical Model Context Protocol

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

Efficient pythonic random access to fasta subsequences

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

A React web application to query and share any PostgreSQL database.

Sequence-to-graph mapper and graph generator

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.

Graph-linked unified embedding for single-cell multi-omics data integration

RAxML Next Generation: faster, easier-to-use and more flexible

Structural variant and indel caller for mapped sequencing data

Haplotype VCF comparison tools

生信爱好者周刊（每周日发布）

A repository for setting up a RNAseq workflow

Library for Digital Pathology Image Processing

Examples of using deep learning in Bioinformatics

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

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

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

CellRank: dynamics from multi-view single-cell data

cython + htslib == fast VCF and BCF processing

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Curated (meta)list of resources for Biology.

🧫 A curated list of resources relevant to doing Biomedical Information Extraction (including BioNLP)

An open source platform for managing and analyzing biomedical big data

Toolset for SV simulation, comparison and filtering

P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

R toolkit for the analysis of single-cell chromatin data

A general, evolvable, and distributed agent framework & harness for data science.

Structural variant toolkit for VCFs

annotate a VCF with other VCFs/BEDs/tabixed files

🦒🦒🦒 Fool-proof, robust, and easy-to-use (robotic-UI-Research)🦒🦒🦒

Align proteins to genomes with splicing and frameshift

A genome visualization python package for comparative genomics

Strelka2 germline and somatic small variant caller

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

DANCE: a deep learning library and benchmark platform for single-cell analysis

BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model | NeurIPS '25

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

code for reading and processing Allen Institute for Brain Science data

Rapid large-scale prokaryote pan genome analysis

:microscope: BEDOPS: high-performance genomic feature operations

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Tools for working with genomic and high throughput sequencing data.