OVESEG
This is the released version of OVESEG; for the devel version, see OVESEG.
OVESEG-test to detect tissue/cell-specific markers
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.28.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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_1.28.0.tar.gz |
| Windows Binary (x86_64) | OVESEG_1.28.0.zip |
| macOS Binary (big-sur-x86_64) | OVESEG_1.28.0.tgz |
| macOS Binary (sonoma-arm64) | OVESEG_1.28.0.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 |