bioinformatics

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. (2025), https://doi.org/10.1093/nar/gkaf361

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

Structural variation caller using third generation sequencing

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

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

ScienceClaw is a personal research assistant built with LangChain DeepAgents and AIO Sandbox infrastructure, adopting a completely new architecture beyond OpenClaw. It offers stronger security, better transparency, and a more user-friendly experience.

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

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

Remote protein homology detection suite.

BioMCP: Biomedical Model Context Protocol

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

Yet another redundant workflow engine

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

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

Biostar Q&A

Cutadapt removes adapter sequences from sequencing reads

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

Open-source bioinformatics components for Dash