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OVESEG

OVESEG-test to detect tissue/cell-specific markers

Bioconductor version: Release (3.17)

An R package for multiple-group comparison to detect tissue/cell-specific marker genes among subtypes. It provides functions to compute OVESEG-test statistics, derive component weights in the mixture null distribution model and estimate p-values from weightedly aggregated permutations. Obtained posterior probabilities of component null hypotheses can also portrait all kinds of upregulation patterns among subtypes.

Author: Lulu Chen <luluchen at vt.edu>

Maintainer: Lulu Chen <luluchen at vt.edu>

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

Installation

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

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

BiocManager::install("OVESEG")

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("OVESEG")
OVESEG User Manual HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBiology, GeneExpression, MultipleComparison, Software
Version 1.16.0
In Bioconductor since BioC 3.9 (R-3.6) (4.5 years)
License GPL-2
Depends R (>= 3.6)
Imports stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp
Linking To Rcpp
Suggests knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales
System Requirements C++11
Enhances
URL
Bug Reports https://github.com/Lululuella/OVESEG
See More
Depends On Me
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Build Report  

Package Archives

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

Source Package OVESEG_1.16.0.tar.gz
Windows Binary OVESEG_1.16.0.zip
macOS Binary (x86_64) OVESEG_1.16.0.tgz
macOS Binary (arm64) OVESEG_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/OVESEG
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/OVESEG
Bioc Package Browser https://code.bioconductor.org/browse/OVESEG/
Package Short Url https://bioconductor.org/packages/OVESEG/
Package Downloads Report Download Stats