bioinformatics

Code examples of fast and simple k-mer counters for tutorial purposes

MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses

SemiBin: metagenomics binning with self-supervised deep learning

tools for analyzing and exploring genetic relationships

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

[ICLR'25] ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Tandem repeat expansion detection or genotyping from long-read alignments

Open source biolab

Cython bindings and Python interface to HMMER3.

sensitive and precise assembly of short sequencing reads

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Genomics Extension for SQLite

Oxbow makes genomic data ready for high-performance analytics.

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works e...

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the...

A simple Snakemake profile for Slurm without --cluster-config

Python library to access Gene Expression Omnibus Database (GEO)

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiang...

SGAS: Sequential Greedy Architecture Search (CVPR'2020) https://www.deepgcns.org/auto/sgas

Biological sequences for the julia language

A modular annotation tool for genomic variants

A fast multiple sequence alignment program.

A fast whole-genome aligner based on de Bruijn graphs

Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full...

WebLogo 3: Sequence Logos redrawn

What should perfect bioinformatic tools be like?

nim wrapper for htslib for parsing genomics data files

Comparing performance-oriented string-processing libraries for substring search, multi-pattern matching, hashing, edit-distances, sketching, and sorti...

A curated list of awesome personal genomics software, libraries, and educational resources.

Tools for processing and analyzing structural variants.

Git-based antigen specificity database storage & management.

Detect and visualize target mutations by scanning FastQ files directly

Bioinformatics library for .NET

an R/shiny application for creation of Circos plot interactively

Single cell analysis in the browser

Drop-in scientific plotting skill for Claude Code, Codex, Cursor, and other coding agents.

Pathogen NGS Documentary

Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in genomes.

📦R包：Make TCGA download and prepare easy!

bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.

Python Programming for Biologists

A genome diagram generator for microbes and organelles

NGLess: NGS with less work

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

BSR-Based Allele Calling Algorithm

accurate LiftOver tool for new genome assemblies

Data visualisation web components for the life sciences.