Anders Valind's repositories
battenberg
Battenberg R package for subclonal copynumber estimation
ossler
A tool for converting affymetrix .oschp-files to .vcf-files.
haplocounter
counting allele specific barcodes
aoc21
Advent of Code 2021 In Rust
gridss
GRIDSS: the Genomic Rearrangement IDentification Software Suite
rtg-tools
RTG Tools: Utilities for accurate VCF comparison and manipulation
hank
Playground for implementing a software 3D engine
pz
Easily handle day to day CLI operation via Python instead of regular Bash programs.
hetcor
Calculate concordant heterozygotes from two samples in a vcf file
copynumber
The "copynumber" R package with support for hg38
doppelganger
A small tool to unbreak bams generated by Sentieon UMI
avalind.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
covid19model
Code for modelling estimated deaths and cases for COVID19.
gdc-tools
Scripts for working with GDC data
sv-explore
Code for exploring somatic SVs from matepair-sequencing using TIDDIT as a variant caller
LOHHLA
Fork of https://bitbucket.org/mcgranahanlab/lohhla
avbio
Various code snippets for bioinformatics
subclonal-enrichment
Analysis for subclonal enrichment of SCNAs
good-toulmin
Experimenting with Good-Toulmin estimators and cancer sequencing data
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)
raekwan
Various tools for doing post processing of called somatic variants.
avlib
Various small snippets of python that I find useful
optitype
Singularity port of OptiType for precision HLA typing from next-generation sequencing data
nexus-manip
Code for extracting data from exported segment tables from Nexus Copy Number 7.5