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

Tools for analyzing DNA methylation data

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

Tandem repeat genotyping and visualization from PacBio HiFi data