avalind

farsbot

pajp

Somatic mutation calling on moderately deep WES data using GATK/MuTect

bloomlada

C++ Implementation of a standard bloom filter, using MurmurHash (v2)

aoc21

Advent of Code 2021 In Rust

avalind.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

avbio

Various code snippets for bioinformatics

avlib

Various small snippets of python that I find useful

battenberg

Battenberg R package for subclonal copynumber estimation

copynumber

The "copynumber" R package with support for hg38

covid-sim

covid19model

Code for modelling estimated deaths and cases for COVID19.

doppelganger

A small tool to unbreak bams generated by Sentieon UMI

evotypes_p1

gdc-tools

Scripts for working with GDC data

good-toulmin

Experimenting with Good-Toulmin estimators and cancer sequencing data

gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite

hank

Playground for implementing a software 3D engine

haplocounter

counting allele specific barcodes

hetcor

Calculate concordant heterozygotes from two samples in a vcf file

LOHHLA

Fork of https://bitbucket.org/mcgranahanlab/lohhla

nexus-manip

Code for extracting data from exported segment tables from Nexus Copy Number 7.5

nxtpipe

optitype

Singularity port of OptiType for precision HLA typing from next-generation sequencing data

ossler

A tool for converting affymetrix .oschp-files to .vcf-files.

polysolver

Singularity port of HLA typing based on an input exome BAM file and is currently infers infers alleles for the three major MHC class I (HLA-A, -B, -C)

pz

Easily handle day to day CLI operation via Python instead of regular Bash programs.

raekwan

Various tools for doing post processing of called somatic variants.

rtg-tools

RTG Tools: Utilities for accurate VCF comparison and manipulation

subclonal-enrichment

Analysis for subclonal enrichment of SCNAs

sv-explore

Code for exploring somatic SVs from matepair-sequencing using TIDDIT as a variant caller