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receptLoss

Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors


Bioconductor version: Release (3.18)

receptLoss identifies genes whose expression is lost in subsets of tumors relative to normal tissue. It is particularly well-suited in cases where the number of normal tissue samples is small, as the distribution of gene expression in normal tissue samples is approximated by a Gaussian. Originally designed for identifying nuclear hormone receptor expression loss but can be applied transcriptome wide as well.

Author: Daniel Pique, John Greally, Jessica Mar

Maintainer: Daniel Pique <daniel.pique at med.einstein.yu.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("receptLoss")

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("receptLoss")
receptLoss HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, Software, StatisticalMethod
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3 + file LICENSE
Depends R (>= 3.6.0)
Imports dplyr, ggplot2, magrittr, tidyr, SummarizedExperiment
System Requirements
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Suggests knitr, rmarkdown, testthat (>= 2.1.0), here
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Package Archives

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

Source Package receptLoss_1.14.0.tar.gz
Windows Binary receptLoss_1.14.0.zip
macOS Binary (x86_64) receptLoss_1.14.0.tgz
macOS Binary (arm64) receptLoss_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/receptLoss
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/receptLoss
Bioc Package Browser https://code.bioconductor.org/browse/receptLoss/
Package Short Url https://bioconductor.org/packages/receptLoss/
Package Downloads Report Download Stats