OVESEG

DOI: 10.18129/B9.bioc.OVESEG    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see OVESEG.

OVESEG-test to detect tissue/cell-specific markers

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	OVESEG User Manual
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBiology, GeneExpression, MultipleComparison, Software
Version	1.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL-2
Depends	R (>= 3.6)
Imports	stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales
SystemRequirements	C++11
Enhances
URL
BugReports	https://github.com/Lululuella/OVESEG
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	OVESEG_1.0.0.tar.gz
Windows Binary	OVESEG_1.0.0.zip
Mac OS X 10.11 (El Capitan)	OVESEG_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/OVESEG
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OVESEG
Package Short Url	https://bioconductor.org/packages/OVESEG/
Package Downloads Report	Download Stats