theJasonFan

snakemake-tutorial

kmers

A bit-packed k-mer representation (and relevant utilities) for rust

simple-sds

Simple succinct data structures (in Rust)

chacon

Commitable HAsh CONtracts.

cuttlefish

Building the compacted de Bruijn graph efficiently from references or reads.

KMC

Fast and frugal disk based k-mer counter

advent-of-code-2020

bamgineer

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

CMSC828O

cmsc858D

Succinct data structures for CMSC858D

criterion.rs

Statistics-driven benchmarking library for Rust

dotfiles

gradual-typing

Implementation of Gradually Typed Lambda Calculus

jf.zsh-theme

kelp

Contig tiling to reference sequence simulator

mazu-pybindings

Testing out python bindings for mazu default indexes

meta-review

Manuscript describing open collaborative writing with Manubot

metagraph-workflows

nf-tower-aws

Repository containing required policies for Nextflow Tower deployment on AWS

nf-wc

`wc` from Nextflow, can be useful for testing deployments

pufferfish

An efficient index for the colored, compacted, de Bruijn graph

pufferfish2

rust-boomphf

Fast and scalable minimal perfect hashing for massive key sets

rust-clippy

A bunch of lints to catch common mistakes and improve your Rust code

scanpy

Single-cell analysis in Python. Scales to >1M cells.

SEQC-data

Download SEQC data - aggregate reads for replicates across flowcellls and sites - rename samples with usable names

shoal

Improved multi-sample transcript abundance estimates using adaptive priors

umd-thesis-template

umdcs-prelim-approval

yay-evil-emacs

😈 A lightweight literate Emacs config with even better "better defaults". Shipped with a custom theme!