doppelgangR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see doppelgangR.

Identify likely duplicate samples from genomic or meta-data

Bioconductor version: 3.21

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 "4.5") 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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, ImmunoOncology, Microarray, QualityControl, RNASeq, Software

Version 1.36.1

In Bioconductor since BioC 3.3 (R-3.3) (9.5 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 https://waldronlab.github.io/doppelgangR

Bug Reports https://github.com/lwaldron/doppelgangR/issues

Suggests BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat

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Package Archives

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

Source Package doppelgangR_1.36.1.tar.gz

Windows Binary (x86_64) doppelgangR_1.36.1.zip

macOS Binary (x86_64) doppelgangR_1.36.1.tgz

macOS Binary (arm64) doppelgangR_1.36.1.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 3.21 Source Archive