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Starred repositories
Examples of my Claude Code infrastructure with skill auto-activation, hooks, and agents
Joint structural variant and copy number variant caller for HiFi sequencing data
Snakemake pipeline for generating and running on new simulated data for HATCHet2 revisions
Solutions to Linear Algebra Done Right, by Sheldon Axler.
Code / solutions for Mathematics for Machine Learning (MML Book)
Various algorithms for analysing genomics data
Tumor-normal variant calling workflow using HiFi reads
A Python-embedded modeling language for convex optimization problems.
This is the official repository for the "doggo dot jl" YouTube channel (fka "julia for talented amateurs").
Additional exercises and data for EE364a. No solutions; for public consumption.
piecewise-regression (aka segmented regression) in python. For fitting straight line models to data with one or more breakpoints where the gradient changes.
A comprehensive catalog of modern and classic books on C++ programming language
Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling
RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes
MASCoTE (Multiple Allele-specific Simulation of Copy-number Tumor Evolution) is a simulation framework to generate sequencing reads with appropriately corrections for the differences in genome leng…
CWL for GDC DNASeq workflows
Reducing reference bias using multiple population reference genomes
HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, a…
Copy number caller for long read data including SNV utilization
Commandline tool for converting between several e-books formats, based on Calibre project.
Integrates the reMarkable tablet into an Obsidian workflow by letting users quickly capture and insert their drawings.