bioinformatics

Global Biotic Interactions provides access to existing species interaction datasets

A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GA...

FABind: Fast and Accurate Protein-Ligand Binding (NeurIPS 2023)

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

Global alignment and alignment extension

Deep Learning-based Clustering Approaches for Bioinformatics

Open-source usearch

Bam Error Stats Tool (best): analysis of error types in aligned reads.

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive b...

A high-performance, pure Rust toolkit for standardizing and preparing biomolecular systems (proteins & nucleic acids). It heals missing atoms, resolve...

Analyze your RNA sequencing data without writing a single line of code

A genome diagram generator for microbes and organelles

Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all

An efficient FASTQ manipulation suite

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

BWA-MEME: Faster BWA-MEM2 using learned-index

Plasmid and primer design software

PANDORA :computer:

Base Classes and Functions for Mass Spectrometry and Proteomics

GATK RNA-Seq Variant Calling in Nextflow

Calculation of interatomic interactions in molecular structures

Tools for single-cell data processing

Bayesian genotyper for structural variants

Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)

Comparative Genomics Toolkit 3

Extract 3D contacts (.pairs) from sequencing alignments

MCP server for 200M+ patents, scientific literature, chemistry and pharma records. Search prior art and R&D intelligence powered by PatSnap's propriet...

A minimalist multi-agent framework for rubost automation of scientific analysis workflows, such as gene expression analysis.

Software for biomolecular electrostatics and solvation calculations

MyGene.info: A BioThings API for gene annotations

python library for working with ontologies and ontology associations

Drop-in scientific plotting skill for Claude Code, Codex, Cursor, and other coding agents.

Parser and database to index the terpene profile of different strains of Cannabis from online databases

An open-access bioinformatics text

APBS - software for biomolecular electrostatics and solvation

Apache cTAKES is a Natural Language Processing (NLP) platform for clinical text.

Gene fusion detection and visualization

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

Benchmark for LLM-based Agents in Computational Biology

BLASR: The PacBio® long read aligner

An app store for scientific workflows, tools, notebooks, and services

BWT construction and search

Cute tricks for SIMD vectorized binary encoding and decoding of nucleotides, in Rust.

A tool for cell instance aware segmentation in densely packed 3D volumetric images

SquiggleKit: A toolkit for manipulating nanopore signal data

A bioinformatic toolkit to align genome assemblies into pangenome graphs

:rocket: seqfu - Sequece Fastx Utilities

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing