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doppelgangR

This is the development version of doppelgangR; for the stable release version, see doppelgangR.

Identify likely duplicate samples from genomic or meta-data


Bioconductor version: Development (3.19)

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 (from within R, enter citation("doppelgangR")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews GeneExpression, ImmunoOncology, Microarray, QualityControl, RNASeq, Software
Version 1.31.0
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, testthat
Linking To
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Package Archives

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

Source Package doppelgangR_1.31.0.tar.gz
Windows Binary doppelgangR_1.31.0.zip
macOS Binary (x86_64) doppelgangR_1.31.0.tgz
macOS Binary (arm64) doppelgangR_1.31.0.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/
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