A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

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

The definitive protocol for Python in computational biology - workshop for CBG Retreat 2026

Tree inference from mitochondrial mutations

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

Fast, scalable, accurate and accessible Bayesian phylogenetics

Repository for the clone2vec python package

The scripts used for analyzing JAX mouse dataset

A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. Stored as pure Python. All in a modern, AI-native editor.

pomodoro technique for org-mode

(GABI) GESTALT Analysis using Bayesian Inference for BEAST2

Inference and analysis of mutation trees in Python

[MIRROR] Emacs support for Snakemake

Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data

A Fast Branch and Bound Algorithm for the Perfect Tumor Phylogeny Reconstruction Problem

Kolmogorov Arnold Networks

Tasty additions to BEAST 2

A probabilistic programming language in TensorFlow. Deep generative models, variational inference.

GESTALT processing pipeline for barcodes captured with single-cell RNA sequencing

A simulator of malaria epidemiology and control

Recurrent Models of Visual Attention (RAM) with Chainer