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OVESEG

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

OVESEG-test to detect tissue/cell-specific markers


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-2
Depends R (>= 3.6)
Imports stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp
System Requirements C++11
URL
Bug Reports https://github.com/Lululuella/OVESEG
See More
Suggests knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales
Linking To Rcpp
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 OVESEG_1.19.0.tar.gz
Windows Binary OVESEG_1.19.0.zip
macOS Binary (x86_64) OVESEG_1.19.0.tgz
macOS Binary (arm64) OVESEG_1.19.0.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