Examples of my Claude Code infrastructure with skill auto-activation, hooks, and agents

Harness engineering beginner tutorial, from 0 to 1

a set of SKILLS.md for doing bioinformatics with agents like claude code

GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other databases and tools.

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

Implementation of the multiple sequential markovian coalescent

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

Mutational signature analysis for low statistics SNV data

GFFBase — Rust+DuckDB GFF3/GTF engine

Multi-sample multi-group scRNA-seq analysis tools

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities i…

Different flavours of CUSUM for change point detection.

Domestication and Improvement Reshaped the Genomic Architecture of Abiotic Stress Tolerance in Sunflower

Official release of OneGenome-Rice models.

Domestication and Improvement Reshaped the Genomic Architecture of Abiotic Stress Tolerance in Sunflower

Tandem repeats annotation tool

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

A fast and flexible algorithm for solving the graph-fused lasso

Python package to run DefensePredictor, a machine learning model to identify proteins involved in anti-phage defense

Scientific Inkscape: Inkscape extensions for figure resizing and editing

GigaTIME: Multimodal AI generates virtual population for tumor microenvironment modeling (Cell)