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>

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

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/
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