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doppelgangR
This is thereleased version of doppelgangR; for the devel version, seedoppelgangR.
Identify likely duplicate samples from genomic or meta-data
Bioconductor version: Release (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("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 appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression,ImmunoOncology,Microarray,QualityControl,RNASeq,Software |
| Version | 1.38.0 |
| 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/doppelgangRhttps://waldronlab.github.io/doppelgangR |
| Bug Reports | https://github.com/lwaldron/doppelgangR/issues |
See More
| Suggests | BiocStyle,knitr,rmarkdown,curatedOvarianData,testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | doppelgangR_1.38.0.tar.gz |
| Windows Binary (x86_64) | doppelgangR_1.38.0.zip |
| macOS Binary (x86_64) | doppelgangR_1.38.0.tgz |
| macOS Binary (arm64) | doppelgangR_1.38.0.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 |