bioinformatics

Python library to facilitate genome assembly, annotation, and comparative genomics

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of t...

🔬🦞 A self-evolving AI research colleague for scientists. 285 skills, zero hallucination, persistent memory.

A curated list of Cheminformatics libraries and software.

The next version of bwa-mem

Specification for the Workflow Description Language (WDL).

Plant phenotyping with image analysis

Precision Medicine Knowledge Graph (PrimeKG)

Bioinformatics containers

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A fast and sensitive gapped read aligner

Python package for graph neural networks in chemistry and biology

Python and C++ code for reading and writing genomics data.

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Annotated data.

Tools to process and analyze deep sequencing data.

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Versatile open-source tool for microbiome analysis

Working with molecular structures in pandas DataFrames

A Go package for engineering organisms.

Ultra-fast and memory-efficient (meta-)genome assembler

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al....

A high-performance, Pythonic language for bioinformatics

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Structural variation caller using third generation sequencing

High-school research portfolio: 2 peer-reviewed publications (IEEE, IJHSR) + 3 active projects spanning quantum-inspired ML, computational biology, bi...

ScienceClaw is a personal research assistant built with LangChain DeepAgents and AIO Sandbox infrastructure, adopting a completely new architecture be...

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

Gene cluster comparison figure generator

A scikit-learn compatible library for graph kernels

BWK awk modified for biological data

BioMCP: Biomedical Model Context Protocol

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Remote protein homology detection suite.

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Tools for working with SAM/BAM data

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

The Chemistry Development Kit

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Signal-level algorithms for MinION data

Yet another redundant workflow engine

:scissors: :zap: Rapid haploid variant calling and core genome alignment

Biostar Q&A

COBRApy is a package for constraint-based modeling of metabolic networks.

Cutadapt removes adapter sequences from sequencing reads

Open-source bioinformatics components for Dash

Accurate sample inference from amplicon data with single nucleotide resolution

Quickly search, compare, and analyze genomic and metagenomic data sets.