An open-source alternative to Claude Cowork, powered by opencode

Genome To Transcriptome re-mapping utility

Creating alignment plots from bam files

A fast multi-threaded k-mer counter

Python utilities for Manubot: Manuscripts, open and automated

A polyglot document intelligence framework with a Rust core. Extract text, metadata, and structured information from PDFs, Office documents, images, and 50+ formats. Available for Rust, Python, Rub…

eCLIP/iCLIP data processing toolkit

Transcript Distance Calculations

An agentic skills framework & software development methodology that works.

Unify transcripts across different samples

R package for building customizable CVs from spreadsheets

Claude Code skill implementing Manus-style persistent markdown planning — the workflow pattern behind the $2B acquisition.

Memray is a memory profiler for Python

A set of ready to use scientific skills for Claude

The Best Agent Harness. Meet Sisyphus: The Batteries-Included Agent that codes like you.

Lightweight and extensible compatibility layer between dataframe libraries!

Finding project directories in Python (data science) projects, just like in R rprojroot and here packages

Override and customize Python packages without touching their code

Intuitive guide to multi-omics integration with toy examples: supervised latent components (DIABLO), unsupervised shared/partial/unique structure (DIVAS), VAEs/conditional VAEs, and key baselines (…

RNA-seq Analysis Pipeline Testing and Optimization Resource - Intelligent pipeline selection and comprehensive benchmarking.

Motif Enrichment In Ranked Lists Of Peaks

a lexicographically-based GTF/GFF sorter

ComBat-ref is a Simple and Highly Effective Batch Effect Correction Method for RNA-seq Count Data

The CSV magician

EnrichMap: Spatially-informed enrichment analysis for functional interpretation of spatial transcriptomics.

Fast Gene Set Enrichment Analysis

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files