RaikOtto/Younikorn: Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

This packages enables users to identify cancer cell lines. Cancer cell line misidentification and cross-contamination reprents a significant challenge for cancer researchers. The identification is vital and in the frame of this package based on the locations/ loci of somatic and germline mutations/ variations. The input format is vcf/ vcf.gz and the files have to contain a single cancer cell line sample (i.e. a single member/genotype/gt column in the vcf file). The implemented method is optimized for the Next-generation whole exome and whole genome DNA-sequencing technology. RNA-seq data is very likely to work as well but hasn't been rigiously tested yet. Panel-seq will require manual adjustment of thresholds

Getting started

Package details

AuthorRaik Otto
Bioconductor views ExomeSeq Software StatisticalMethod WholeGenome
Maintainer'Raik Otto' <[email protected]>
LicenseArtistic-2.0
Version2.1.4
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("RaikOtto/Younikorn")
RaikOtto/Younikorn documentation built on Oct. 14, 2018, 7:13 p.m.