RankProd
This is the released version of RankProd; for the devel version, see RankProd.
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Bioconductor version: Release (3.23)
Non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). The method can combine data sets from different origins (meta-analysis) to increase the power of the identification.
Author: Francesco Del Carratore <francesco.delcarratore at manchester.ac.uk>, Andris Jankevics <andris.jankevics at gmail.com> Fangxin Hong <fxhong at jimmy.harvard.edu>, Ben Wittner <Wittner.Ben at mgh.harvard.edu>, Rainer Breitling <rainer.breitling at manchester.ac.uk>, and Florian Battke <battke at informatik.uni-tuebingen.de>
Maintainer: Francesco Del Carratore <francescodc87 at gmail.com>
citation("RankProd")):
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("RankProd")
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("RankProd")| RankProd Tutorial | R Script | |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSignaling, Lipidomics, Metabolomics, Microarray, Proteomics, ResearchField, Software, StatisticalMethod, SystemsBiology |
| Version | 3.38.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | file LICENSE |
| Depends | R (>= 3.2.1), stats, methods, Rmpfr, gmp |
| Imports | graphics |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | tRanslatome |
| Imports Me | mslp, POMA, synlet |
| Suggests Me | pepdiff |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RankProd_3.38.0.tar.gz |
| Windows Binary (x86_64) | RankProd_3.38.0.zip |
| macOS Binary (big-sur-x86_64) | RankProd_3.38.0.tgz |
| macOS Binary (sonoma-arm64) | RankProd_3.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RankProd |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RankProd |
| Bioc Package Browser | https://code.bioconductor.org/browse/RankProd/ |
| Package Short Url | https://bioconductor.org/packages/RankProd/ |
| Package Downloads Report | Download Stats |