Uniquorn
This is the development version of Uniquorn; for the stable release version, see Uniquorn.
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
Bioconductor version: Development (3.24)
'Uniquorn' 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).
Author: Raik Otto
Maintainer: Raik Otto <raik.otto at hu-berlin.de>
citation("Uniquorn")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | ExomeSeq, ImmunoOncology, Software, StatisticalMethod, WholeGenome |
| Version | 2.33.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5) |
| Imports | stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation, data.table |
| System Requirements | |
| URL |
See More
| Suggests | testthat, knitr, rmarkdown, BiocGenerics |
| 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_2.33.0.tar.gz |
| Windows Binary (x86_64) | Uniquorn_2.33.0.zip |
| macOS Binary (big-sur-x86_64) | Uniquorn_2.33.0.tgz |
| macOS Binary (sonoma-arm64) | Uniquorn_2.33.0.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 |