Uniquorn

This package is for version 3.9 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: 3.9

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>

Citation (from within R, enter citation("Uniquorn")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Uniquorn")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Uniquorn")
Uniquorn vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExomeSeq, ImmunoOncology, Software, StatisticalMethod, WholeGenome
Version 2.4.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License Artistic-2.0
Depends R (>= 3.5)
Imports stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation
System Requirements
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Suggests testthat, knitr, rmarkdown, BiocGenerics, RUnit
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Uniquorn_2.4.0.tar.gz
Windows Binary Uniquorn_2.4.0.zip
Mac OS X 10.11 (El Capitan) Uniquorn_2.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Uniquorn
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Uniquorn
Bioc Package Browser https://code.bioconductor.org/browse/Uniquorn/
Package Short Url https://bioconductor.org/packages/Uniquorn/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive