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Code & Additional Materials from the T2T Marmoset Project
Run many Claude Code sessions across your projects, each in its own tmux session — then list them, see which are done vs. still working, and jump to one from a single popup.
Mapping sequencing data to De Bruijn graphs, fast
Terminal-based plasmid map viewer, sequence editor, and cloning/mutagenesis workbench in pure Python
Code for Command-Line Rust (O'Reilly, 2024, ISBN 9781098109417)
A shell language with cleaner syntax, automatic redirection, and proper datatypes
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
Processing and analysis pipelines for the manuscript titled "Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania"
Color palette package in R inspired by works at the Metropolitan Museum of Art in New York
ggideogram is a ggplot2 extension package for drawing chromosome diagrams
An extensible and performant aligner and read mapper
An all-singing, all-dancing, bash template for cool CLI scripts (a bash cookiecutter).
Just a collection of (often poor) scripts to do various bits of bioinformatics stuff I find myself needing to do.
Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments
R package for modeling single cell UMI expression data using regularized negative binomial regression
rapids-singlecell: GPU-accelerated framework for scRNA analysis
All code necessary for reconstructing Bonsai-trees on high-dimensional data and visualizing them in Bonsai-scout