avalind Goto Github PK

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

bloomlada

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

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

farsbot

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

numenor

A Simple N-body simulation in python.

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.

pajp

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

particles

Me playing around with game physics.

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