bioinformatics
Repositories (1500)
A fast tool for detecting and decomposing segmental duplications in genome assemblies
Open-source precision oncology platform that ranks FDA-approved and repurposing drug candidates from a patient's variant profile using OncoKB, AlphaMi...
Various utilities regarding Levenshtein transducers. (Java)
Protein Alignment and Detection Interface
slurmR: A Lightweight Wrapper for Slurm
Cloud engine and platform for metabolite annotation for imaging mass spectrometry
Useful bioinformatic scripts
VAPiD: Viral Annotation and Identification Pipeline
:books: Various bioinformatics tutorials
Bioinformatics on GCP, AWS or Azure
Reference-based consensus creation
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
A curated list of awesome self-learning materials in Computational Structural Biology, such as sources, tutorials, etc.
A Rust-based, headless workflow execution framework supporting local, cloud, and HPC.
High-performance UMI tools for NGS data analysis
The bioinformatics agent desktop for clinicians and wet-lab scientists — built on DeepSeek Harness. One-click installers, a skill store, offline mode.
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
Remove contaminated contigs from genomes using k-mers and taxonomies.
Efficient target prediction incorporating accessibility of interaction sites
Variant Calling Pipeline Using GATK4 and Nextflow
A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX...
quickly filter fastq files by matching sequences to a set of regex patterns
Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
Support Vector Structural Variation Genotyper
Pattern Recognition for Cell-free DNA
Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)
A Python platform for Structural Bioinformatics
de novo virus assembler of Illumina paired reads
Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
A server implementation of the htsget protocol for bioinformatics in Rust
Frequently used commands in bioinformatics
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable E...
⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.
An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
A curated list of awesome AI and Bioinformatics.
A manifesto for AI-assisted modernisation of bioinformatics software.
Multimodal foundation model predicting transcriptome-wide virtual spatial transcriptomics from histology.
Lightweight Iterative Gene set Enrichment in R
sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java
List of IARC bioinformatics pipelines and resources
DeepMosaic is a deep-learning-based mosaic single nucleotide classification tool without the need of matched control information.
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.
Comprehensive Python client for the Uniprot REST API
A community-focused repository dedicated to fostering learning and development in Artificial Intelligence 🚀. This project, created by me, @nath.bioha...
🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖...
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
Transmembrane proteins predicted through Language Model embeddings