OVESEG

DOI: 10.18129/B9.bioc.OVESEG    

This is the development version of OVESEG; to use it, please install the devel version of Bioconductor.

OVESEG-test to detect tissue/cell-specific markers

Bioconductor version: Development (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

HTML R Script OVESEG User Manual
PDF   Reference Manual
Text   NEWS

Details

biocViews CellBiology, GeneExpression, MultipleComparison, Software
Version 1.1.0
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
Links To Me
Build Report  

Package Archives

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

Source Package OVESEG_1.1.0.tar.gz
Windows Binary OVESEG_1.1.0.zip
Mac OS X 10.11 (El Capitan) OVESEG_1.1.0.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 http://bioconductor.org/packages/OVESEG/
Package Downloads Report Download Stats

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