bioinformatics
Repositories (1438)
Graph-based mapping of long sequences, noisy or HiFi.
The Ensembl Compara Perl API and SQL schema
A fast and scalable phylogenetic tree viewer for microbiome data analysis
Fast and Accurate CE-, GC- and LC-MS(/MS) Data Processing
CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
The Enhanced Database of Interacting Protein Structures for Interface Prediction
AI and Omics Research Internship 2025
A community-focused repository dedicated to fostering learning and development in Artificial Intelligence 🚀. This project, created by me, @nath.bioha...
Emperor a tool for the analysis and visualization of large microbial ecology datasets
Natural language processing of Gene Expression Omnibus data
Curated list of bioinformatics formats and publications
HTS-compatible wrapper for IgBlast V-(D)-J mapping tool
CLI for interacting with Cromwell servers
Deep (Transfer) Learning for Peptide Retention Time Prediction
Interpretation of proteomics identification results
Data structures, algorithms, and parsing for crystallography
🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data
A Python implementation for BH-FDR and HiCCUPS
GNparser normalises scientific names and extracts their semantic elements.
genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from...
Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches
🔬🖥 Automated Blood Vasculature Analysis of 3D Light-Sheet Image Volumes
🧬 Toolkit for generating various numerical features of protein sequences
This library tackles the construction and efficient execution of computational chemistry workflows
Python package and command line tool for epitope prediction
GNfinder finds scientific names in UTF8 texts, PDF files, MS Word/Excel documents, URLs etc.
A versatile compressor of third generation sequencing reads.
This repository contains Docker files for the images maintained by the Phenotypic Evolution Group at the Institute for Molecular and Cell Biology / In...
DeepMosaic is a deep-learning-based mosaic single nucleotide classification tool without the need of matched control information.
A lightweight and powerful Julia package for computational pipelines and workflows.
An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
BioContainers specifications
Cloud-based single-cell copy-number variation analysis tool
Pipeline for structural variation detection in cohorts
Phigaro is a scalable command-line tool for predicting phages and prophages
Multiple-particle tracking designed to (1) track dense particle fields, (2) close gaps in particle trajectories resulting from detection failure, and...
A python package and a set of shell commands to handle GTF files
Efficient target prediction incorporating accessibility of interaction sites
:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)
Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and...
Democratizing ML in proteomics
ChatCell: Facilitating Single-Cell Analysis with Natural Language
A curated list of awesome AI and Bioinformatics.
Functionality for working with pipeline and sample sheet schema files in Nextflow pipelines
A Rust-based, headless workflow execution framework supporting local, cloud, and HPC.
Fast, Accurate and Memory-Efficient Principal Component Analysis All in One For Large-scale Dataset