doppelgangR

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Identify likely duplicate samples from genomic or meta-data

Bioconductor version: Development (3.24)

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")):

Levi Waldron, Markus Reister. doppelgangR: Identify likely duplicate samples from genomic or meta-data. doi:10.18129/B9.bioc.doppelgangR, R package version 1.41.2, https://bioconductor.org/packages/doppelgangR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, ImmunoOncology, Microarray, QualityControl, RNASeq, Software
Version	1.41.2
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	GPL (>=2.0)
Depends	R (>= 3.5.0), Biobase
Imports	future, future.apply, 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, S4Vectors
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	doppelgangR_1.41.2.tar.gz
Windows Binary (x86_64)	doppelgangR_1.41.2.zip
macOS Binary (big-sur-x86_64)	doppelgangR_1.41.2.tgz
macOS Binary (sonoma-arm64)	doppelgangR_1.41.2.tgz
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