bioinformatics

A lightweight and powerful Julia package for computational pipelines and workflows.

AI and Omics Research Internship 2025

A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from...

RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches

Fast, Accurate and Memory-Efficient Principal Component Analysis All in One For Large-scale Dataset

Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data

Repository to propose and discuss lineages

충남대학교 김준 연구실 튜토리얼

Activity-Oriented Enzyme Sequence Design by Steered Inverse Protein Folding

An agent that takes a dead research repo and turns it into a callable pipeline component.

Natural language processing of Gene Expression Omnibus data

BioContainers specifications

🧬 Toolkit for generating various numerical features of protein sequences

Deep (Transfer) Learning for Peptide Retention Time Prediction

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 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...

Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and...

Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data

StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy

Minimizer-based assembly scaffolding and mapping using long reads

A tool for the recovery of unassembled telomeres from soft-clipped read alignments.

Meet FIORA! An in silico fragmentation algorithm designed to predict tandem mass spectra (MS/MS) with high accuracy. Using graph neural networks, FIOR...

Information-Theoretic Measures for Revealing Variable Interactions

A manifesto for AI-assisted modernisation of bioinformatics software.

Collection of commonly used RDP Tools for easy building

Cloud-based single-cell copy-number variation analysis tool

Pipeline for structural variation detection in cohorts

an implementation of NSGA-II in java

non-redundant, compressed, journalled, file-based storage for biological sequences

A python package and a set of shell commands to handle GTF files

Precision psychophysiology made easy

Fast and flexible semi-supervised learning for peptide detection in Python

Close assembly gaps using long-reads at high accuracy.

:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)

Claude-Code for Bioinformatics

Tool suite for HGVS variant descriptions

BRIG is a cross-platform (Windows/Mac/Linux) application that displays circular comparison images of multiple genomes using BLAST.

A fragment-based molecular assembly toolkit

Parse Illumina sample sheets with Python

Exact Tandem Repeat Finder (not a TRF replacement)

A simple command-line tool to download data from Joint Genome Institute databases

A reimplementation of the WaveFront Alignment algorithm at low memory

Identifying tumor cells at the single-cell level using machine learning

A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

ChatCell: Facilitating Single-Cell Analysis with Natural Language

Remove human reads from a sequencing run

Transmembrane proteins predicted through Language Model embeddings

CellNavi is a deep learning framework designed to predict genes driving cellular transitions.