Pinned Repositories
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)
farsbot
Numenor
A Simple N-body simulation in python.
pajp
Somatic mutation calling on moderately deep WES data using GATK/MuTect
particles
Me playing around with game physics.
avalind's Repositories
avalind/farsbot
avalind/pajp
Somatic mutation calling on moderately deep WES data using GATK/MuTect
avalind/bloomlada
C++ Implementation of a standard bloom filter, using MurmurHash (v2)
avalind/aoc21
Advent of Code 2021 In Rust
avalind/avalind.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
avalind/avbio
Various code snippets for bioinformatics
avalind/avlib
Various small snippets of python that I find useful
avalind/battenberg
Battenberg R package for subclonal copynumber estimation
avalind/copynumber
The "copynumber" R package with support for hg38
avalind/covid-sim
avalind/covid19model
Code for modelling estimated deaths and cases for COVID19.
avalind/doppelganger
A small tool to unbreak bams generated by Sentieon UMI
avalind/evotypes_p1
avalind/gdc-tools
Scripts for working with GDC data
avalind/good-toulmin
Experimenting with Good-Toulmin estimators and cancer sequencing data
avalind/gridss
GRIDSS: the Genomic Rearrangement IDentification Software Suite
avalind/hank
Playground for implementing a software 3D engine
avalind/haplocounter
counting allele specific barcodes
avalind/hetcor
Calculate concordant heterozygotes from two samples in a vcf file
avalind/LOHHLA
Fork of https://bitbucket.org/mcgranahanlab/lohhla
avalind/nexus-manip
Code for extracting data from exported segment tables from Nexus Copy Number 7.5
avalind/nxtpipe
avalind/optitype
Singularity port of OptiType for precision HLA typing from next-generation sequencing data
avalind/ossler
A tool for converting affymetrix .oschp-files to .vcf-files.
avalind/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)
avalind/pz
Easily handle day to day CLI operation via Python instead of regular Bash programs.
avalind/raekwan
Various tools for doing post processing of called somatic variants.
avalind/rtg-tools
RTG Tools: Utilities for accurate VCF comparison and manipulation
avalind/subclonal-enrichment
Analysis for subclonal enrichment of SCNAs
avalind/sv-explore
Code for exploring somatic SVs from matepair-sequencing using TIDDIT as a variant caller