edawson

gfakluge

A C++ library and utilities for manipulating the Graphical Fragment Assembly format.

svaha

Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]

pliib

A hacky little C++ library that holds some useful functions.

sv-exercise-1

A short exercise for learning to work with structural variants in VCF format

bam-matcher

kseqpp

Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)

sv-tutorial-2

A tutorial on calling structural variants with SVABA

tinyFA

A header-only C++ FASTA parser and indexer

1brc

1️⃣🐝🏎️ The One Billion Row Challenge -- A fun exploration of how quickly 1B rows from a text file can be aggregated with Java

compact_vector

Bit packed vector of integral values

cromrunner

A scheduler / meta-manager for running multiple Cromwell instances on a single WDL workflow in parallel.

cromwell-accountant

A script to calculate estimated cost of a Cromwell workflow on Google Cloud

dawdl

WDL library for common bioinformatics tasks

enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

examples

A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.

gatk

Official code repository for GATK versions 4 and up

helpy

A random collection of python scripts which are easier than fighting the equivalent shell commands

hugo-serif-theme

Serif is a modern business theme for Hugo.

mio

Cross-platform C++11 header-only library for memory mapped file IO

pip2poetry

Convert a requirements.txt file to a poetry.lock file

presig

Convert MAF files to formats used as input to mutational signature programs including SigProfiler

ProteinMPNN

Code for the ProteinMPNN paper

puretabix

r2-public-worker

Cloudflare Worker to make a R2 Bucket public!

RatesTools

Pipeline to calculate de novo mutation rates from parent-offspring trios

saas

Build your own SaaS business with SaaS boilerplate. Productive stack: React, Material-UI, Next, MobX, WebSockets, Express, Node, Mongoose, MongoDB. Written with TypeScript.

SigProfilerHelper

Helper scripts for the SigProfiler suite of mutational signature analysis tools

Spectre

Copy number caller for long read data including SNV utilization

storage-consumption-calculator

An R shiny app for calculating the energy used when storing a specified amount of data.

svaba

Structural variation and indel detection by local assembly