DOI: 10.18129/B9.bioc.Uniquorn    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Uniquorn.

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

Bioconductor version: 3.12

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

Author: Raik Otto

Maintainer: 'Raik Otto' <raik.otto at hu-berlin.de>

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biocViews ExomeSeq, ImmunoOncology, Software, StatisticalMethod, WholeGenome
Version 2.10.0
In Bioconductor since BioC 3.3 (R-3.3) (5 years)
License Artistic-2.0
Depends R (>= 3.5)
Imports stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation
Suggests testthat, knitr, rmarkdown, BiocGenerics, RUnit
Depends On Me
Imports Me
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