bioinformatics

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

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

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

Split k-mer analysis – version 2

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

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

Python programs for processing GFF3 files

Rapid determination of appropriate reference genomes.

A package for designing compact and comprehensive capture probe sets.

Grep for FASTQ files

An interactive web tool for quality control of DNA sequencing data

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

Evidence-linked Palette Fusion for distinctive, editable, and print-ready academic posters.

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

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

Fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, comparison): 16 million viral contigs analyzed in less than an hour...

Biopython Jupyter Notebook tutorial to characterize a small genome

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

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

Command line utility for manipulating FASTQ files

An aviary-based data science agent based on jupyter notebooks

Practical, reusable scripts for bioinformatics

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

Bring your single-cell data to life

Characterization of Germline variants

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....

FastOMA is a scalable software package to infer orthology relationship.

Structural Quality Assessment for Biomolecular Structure Prediction Models

Compacted and colored de Bruijn graph construction and querying

DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xen...

Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5

Segmented HAPlotype Estimation and Imputation Tool

compacted de Bruijn graph construction in low memory

Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome

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

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

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

Protein structure alignment and search algorithm

Auditable bioinformatics workflow compiler: Catalog-bound planning, Workflow IR, and validated WDL 1.0.

Same species annotation lift over pipeline.

Software for predicting library complexity and genome coverage in high-throughput sequencing.

A lightweight and high-performance bioinformatics package in Golang

PacBio® variant and consensus caller

ProtFlash: A lightweight protein language model

My solution to Bioinformatics Specialization (Finding Hidden Messages in DNA; Genome Sequencing; Comparing Genes, Proteins, and Genomes; Molecular Evo...

Rapid standardisation and quality control of GWAS or QTL summary statistics

Predict AMPs in (meta)genomes and peptides

Extensible specification for representing and uniquely identifying biological sequence variation

MyVariant.info: A BioThings API for human variant annotations

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