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 (3.20)
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 "4.4") 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")
doppelgangR vignette | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | GeneExpression, ImmunoOncology, Microarray, QualityControl, RNASeq, Software |
Version | 1.33.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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/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
Follow Installation instructions to use this package in your R session.
Source Package | doppelgangR_1.33.0.tar.gz |
Windows Binary | doppelgangR_1.33.0.zip (64-bit only) |
macOS Binary (x86_64) | doppelgangR_1.33.0.tgz |
macOS Binary (arm64) | doppelgangR_1.33.0.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 |