discordant
This is the development version of discordant; for the stable release version, see discordant.
The Discordant Method: A Novel Approach for Differential Correlation
Bioconductor version: Development (3.24)
Discordant is an R package that identifies pairs of features that correlate differently between phenotypic groups, with application to -omics data sets. Discordant uses a mixture model that “bins” molecular feature pairs based on their type of coexpression or coabbundance. Algorithm is explained further in "Differential Correlation for Sequencing Data"" (Siska et al. 2016).
Author: Charlotte Siska [aut], McGrath Max [aut, cre], Katerina Kechris [aut, cph, ths]
Maintainer: McGrath Max <max.mcgrath at ucdenver.edu>
citation("discordant")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("discordant")
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("discordant")| The discordant R Package: A Novel Approach to Differential Correlation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, Genetics, ImmunoOncology, Microarray, RNASeq, Software, StatisticalMethod, mRNAMicroarray |
| Version | 1.37.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0) |
| Imports | Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr, methods, utils |
| System Requirements | |
| URL | https://github.com/siskac/discordant |
See More
| Suggests | BiocStyle, knitr, testthat (>= 3.0.0) |
| 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 | discordant_1.37.0.tar.gz |
| Windows Binary (x86_64) | discordant_1.37.0.zip |
| macOS Binary (big-sur-x86_64) | discordant_1.37.0.tgz |
| macOS Binary (sonoma-arm64) | discordant_1.37.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/discordant |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/discordant |
| Bioc Package Browser | https://code.bioconductor.org/browse/discordant/ |
| Package Short Url | https://bioconductor.org/packages/discordant/ |
| Package Downloads Report | Download Stats |