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("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 | ||
| 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 | |
| URL |
See More
| Suggests | testthat, knitr, rmarkdown, BiocGenerics, RUnit |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| 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 |