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Bioconductor - doppelgangR (development version)

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 (3.22)

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")

# 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")
Details biocViews GeneExpression, ImmunoOncology, Microarray, QualityControl, RNASeq, Software Version 1.37.3 In Bioconductor since BioC 3.3 (R-3.3) (9 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 See More Package Archives

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

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