OVESEG

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see OVESEG.

OVESEG-test to detect tissue/cell-specific markers

Bioconductor version: 3.21

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBiology, GeneExpression, MultipleComparison, Software

Version 1.24.0

In Bioconductor since BioC 3.9 (R-3.6) (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

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_1.24.0.tar.gz

Windows Binary (x86_64) OVESEG_1.24.0.zip

macOS Binary (x86_64) OVESEG_1.24.0.tgz

macOS Binary (arm64) OVESEG_1.24.0.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/

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