kvg

MosaicAligner

Gil's HMM-based alignment/recombination software from Zilversmit et al. 2013.

notebooks

A Python notebook playground

aou-lr

Analysis workflows for AoU long reads

badges

:pencil: Markdown code for lots of small badges :ribbon: :pushpin: (shields.io, forthebadge.com etc) :sunglasses:. Contributions are welcome! Please add yours!

cortex_tools_benchmark

For benchmarking cortexpy and cortexjdk

CtDNATools

Official code repository for GATK versions 4 and up

dmpy

DistributedMake for Python

mccortex

Cortex on steroids: for larger populations with better assembly

DM

DistributedMake - a perl library for pipelining with GNU make

kvg.github.io

NovelExonFinder

Uses CortexJDK to find novel exons in a transcriptome graph

PacBio

Assessments of PacBio datasets

PedanticCoalescentBook

A coalescent textbook with much more detailed derivations than usually found in treatments of coalescent theory.

pytorch-examples

Playing with PyTorch

pytorch-rust-study

readsim

Simulate DNA sequencing reads using real reads

Repro

Repro: a tool for setting up a reproducible analysis directory

sequence_gan

Generative adversarial networks (GAN) applied to sequential data via recurrent neural networks (RNN).

StatisticalRethinking

Solutions to McElreath's Statistical Rethinking textbook

Writing

Repository of writing (dissertation, articles, literature reviews, etc.)