dN/dS methods to quantify selection in cancer and somatic evolution

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

An analysis toolkit for single-cell methylation sequencing data

Summarize cohort-level TR properties

Data for book

Creating alignment plots from bam files

Shiny Interactive Web Apps for Single-Cell Data

Tools for single-cell data processing

A battery of methylation tools for PacBio HiFi reads

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

Long read production pipelines

Ultimate Plumber is a tool for writing Linux pipes with instant live preview

The repo for the manuscript "Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation"

Algorithm to count repeat size

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency

A complete diploid human genome

Variant calling tool for long-read sequencing data

A structural variation pipeline for short-read sequencing

GPT4All: Run Local LLMs on Any Device. Open-source and available for commercial use.

Generate 3D objects conditioned on text or images

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

A toolset for profiling alternative splicing events in RNA-Seq data.

List of Computer Science courses with video lectures.

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosin…

ShellCheck, a static analysis tool for shell scripts

TRGT Repeat expansion summary