bioinformatics

An analysis and visualization platform for 'omics data

React component for Cytoscape.js network visualisations

d3 library to build circular graphs

Java utilities for Bioinformatics

A curated list of resources for learning bioinformatics.

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

Genome assembly evaluation tool

Bioinformatics one liners from Ming Tang

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

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

Efficient pythonic random access to fasta subsequences

Sequence-to-graph mapper and graph generator

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

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

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

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

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

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

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

Haplotype VCF comparison tools

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

Structural variant and indel caller for mapped sequencing data

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

Library for Digital Pathology Image Processing

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

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

A repository for setting up a RNAseq workflow

生信爱好者周刊（每周日发布）

Curated (meta)list of resources for Biology.

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

Examples of using deep learning in Bioinformatics

CellRank: dynamics from multi-view single-cell data

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http...

Combined RNA and ATAC Footprint Training of Gene Regulatory Network

cython + htslib == fast VCF and BCF processing

Command-first ATAC-seq footprinting, motif analysis, and reproducible interactive reports

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

R toolkit for the analysis of single-cell chromatin data

Toolset for SV simulation, comparison and filtering

A genome visualization python package for comparative genomics

Structural variant toolkit for VCFs

An open source platform for managing and analyzing biomedical big data

Align proteins to genomes with splicing and frameshift

AI-Powered Bioinformatics Research Assistant. Built on OpenClaw.

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

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

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

annotate a VCF with other VCFs/BEDs/tabixed files

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

code for reading and processing Allen Institute for Brain Science data