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aroma.affymetrix

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

ascat

ASCAT copy number R package

ascatngs

Somatic copy number analysis using WGS paired end wholegenome sequencing

dockstore-cgpwgs

Dockstore implementation of CGP core WGS analysis

dramp2.0

Scripts for code of DRAMP 2.0 manuscript submitted to Sci Data

facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

facets-suite

Utility functions for FACETS

gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite

hyperfine

A command-line benchmarking tool

lopez_etal_2019_wgd-cancer

manta

Structural variant and indel caller for mapped sequencing data

methyscan

MethyScan: A tool for methylation specific PCR primer design and evaluation

morpheus.r

R interface to morpheus.js heatmap widget

msisensor

microsatellite instability detection using tumor only or paired tumor-normal data

msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

msisensor2

Microsatellite instability (MSI) detection for tumor only data.

pascal

Performance ASsesment of Copy number alteration calling ALgorithms: pipeline that aims to assess the accuracy of commonly used algorithms for calling copy number alterations from Affymetrix SNP 6.0 array data.

penncnv

Copy number vaiation detection from SNP arrays

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

scripts

sgz

somvarius

Somatic variant identification from unpaired samples

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

wgd

Python package and CLI for whole-genome duplication related analyses