doppelgangR
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see doppelgangR.
Identify likely duplicate samples from genomic or meta-data
Bioconductor version: 3.8
The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).
Author: Levi Waldron [aut, cre], Markus Reister [aut, ctb], Marcel Ramos [ctb]
Maintainer: Levi Waldron <lwaldron.research at gmail.com>
citation("doppelgangR")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("doppelgangR")
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("doppelgangR")| doppelgangR vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, ImmunoOncology, Microarray, QualityControl, RNASeq, Software |
| Version | 1.10.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL (>=2.0) |
| Depends | R (>= 3.5.0), Biobase, BiocParallel |
| Imports | sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils |
| System Requirements | |
| URL | https://github.com/lwaldron/doppelgangR |
| Bug Reports | https://github.com/lwaldron/doppelgangR/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC, RUnit, simulatorZ, proxy |
| 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 | doppelgangR_1.10.1.tar.gz |
| Windows Binary | doppelgangR_1.10.1.zip |
| Mac OS X 10.11 (El Capitan) | doppelgangR_1.10.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/doppelgangR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/doppelgangR |
| Bioc Package Browser | https://code.bioconductor.org/browse/doppelgangR/ |
| Package Short Url | https://bioconductor.org/packages/doppelgangR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |