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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("doppelgangR")
In most cases, you don't need to download the package archive at all.
doppelgangR
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see doppelgangR.
Identify likely duplicate samples from genomic or meta-data
Bioconductor version: 3.3
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, Markus Riester, Marcel Ramos
Maintainer: Levi Waldron <lwaldron.research at gmail.com>
Citation (from within R,
enter citation("doppelgangR")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("doppelgangR")
Documentation
| HTML | R Script | doppelgangR vignette |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, Microarray, QualityControl, RNASeq, Software |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| License | GPL (>=2.0) |
| Depends | R (>= 3.3), Biobase, BiocParallel |
| Imports | sva, impute, digest, mnormt, methods, grDevices, graphics, stats, utils |
| LinkingTo | |
| Suggests | BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC, RUnit, simulatorZ, proxy |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/lwaldron/doppelgangR |
| BugReports | https://github.com/lwaldron/doppelgangR/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | doppelgangR_1.0.2.tar.gz |
| Windows Binary | doppelgangR_1.0.2.zip |
| Mac OS X 10.9 (Mavericks) | doppelgangR_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/doppelgangR/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/doppelgangR/ |
| Package Downloads Report | Download Stats |
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