doppelgangR

DOI: 10.18129/B9.bioc.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 (3.18)

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>

Installation

To install this package, start R (version "4.3") 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

PDF		Reference Manual

Details

biocViews	GeneExpression, ImmunoOncology, Microarray, QualityControl, RNASeq, Software
Version	1.29.0
In Bioconductor since	BioC 3.3 (R-3.3) (7 years)
License	GPL (>=2.0)
Depends	R (>= 3.5.0), Biobase, BiocParallel
Imports	sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat
SystemRequirements
Enhances
URL	https://github.com/lwaldron/doppelgangR
BugReports	https://github.com/lwaldron/doppelgangR/issues
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/doppelgangR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/doppelgangR
Package Short Url	https://bioconductor.org/packages/doppelgangR/
Package Downloads Report	Download Stats