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>
citation("OVESEG")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | CellBiology, GeneExpression, MultipleComparison, Software |
| Version | 1.0.0 |
| 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_1.0.0.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 [email protected]:packages/OVESEG |
| Bioc Package Browser | https://code.bioconductor.org/browse/OVESEG/ |
| Package Short Url | https://bioconductor.org/packages/OVESEG/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |