bioinformatics

Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!

modular & open DIA search

Config files used to define parameters specific to compute environments at different Institutions

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Quantum Mechanical Bespoke Force Field Derivation Toolkit

ClairS - a deep-learning method for long-read somatic small variant calling

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

Fast hash function for DNA/RNA sequences

Code to compute the XP-CLR statistic to infer natural selection

A Julia package to read, write and manipulate macromolecular structures

We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.

A hybrid assembly and MAG recovery pipeline (and more!)

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

WtP: Phage identification via nextflow and docker or singularity

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), t...

(Meta-)genome screening for functional and natural product gene sequences

Split k-mer analysis – version 2

An interactive web tool for quality control of DNA sequencing data

☁️Haven GRC - easier governance, risk, and compliance 👨‍⚕️👮‍♀️🦸‍♀️🕵️‍♀️👩‍🔬

bioinformatics toolkit in rust

Grep for FASTQ files

DeepMicrobes: taxonomic classification for metagenomics with deep learning

Python programs for processing GFF3 files

Local version of the virus identification and analysis web server (tool set)

The Ontology for Biomedical Investigations

Practical, reusable scripts for bioinformatics

High-Performance FASTQ Parsing for Mojo — Zero-Copy to GPU

Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress....

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length seq...

Rapid determination of appropriate reference genomes.

A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

Segmented HAPlotype Estimation and Imputation Tool

Biopython Jupyter Notebook tutorial to characterize a small genome

Pure-python implementation of UCSC liftOver genome coordinate conversion

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

Characterization of Germline variants

compacted de Bruijn graph construction in low memory

Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and Convolutional-LSTM Network

Aim to be the bioinformatics repository with more and newer packages https://doi.org/10.1093/bioinformatics/btaf106

Searching for structural similarities across billions of molecules in milliseconds

BUSCO_Phylogenomics | Pipeline to construct species phylogenies using BUSCO proteins

An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

High performance data storage for importing, querying and transforming variants.

The repository for the Machine Learning and Big Data with kdb+/q book by Novotny et al.

Single Rust: Pioneering single-cell analysis with Rust's concurrency for scalable, high-throughput pipelines. 🧬🚀

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping