Rediscover: Identify Mutually Exclusive Mutations

An optimized method for identifying mutually exclusive genomic events. Its main contribution is a statistical analysis based on the Poisson-Binomial distribution that takes into account that some samples are more mutated than others. See [Canisius, Sander, John WM Martens, and Lodewyk FA Wessels. (2016) "A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence." Genome biology 17.1 : 1-17. <doi:10.1186/s13059-016-1114-x>]. The mutations matrices are sparse matrices. The method developed takes advantage of the advantages of this type of matrix to save time and computing resources.

Version:	0.3.3
Depends:	R (≥ 4.0), Matrix, PoissonBinomial, ShiftConvolvePoibin, utils, matrixStats
Imports:	maftools, data.table, parallel, RColorBrewer, methods
Suggests:	knitr, rmarkdown, RUnit, BiocStyle, dplyr, kableExtra, magick, qvalue, testthat (≥ 3.0.0)
Published:	2025-12-19
DOI:	10.32614/CRAN.package.Rediscover
Author:	Juan A. Ferrer-Bonsoms [aut, cre], Laura Jareno [aut], Angel Rubio [aut]
Maintainer:	Juan A. Ferrer-Bonsoms <jafhernandez at tecnun.es>
License:	Artistic-2.0
NeedsCompilation:	no
Citation:	Rediscover citation info
Materials:	README, NEWS
CRAN checks:	Rediscover results

Documentation:

Reference manual:	Rediscover.html , Rediscover.pdf
Vignettes:	Rediscover (source, R code)

Downloads:

Package source:	Rediscover_0.3.3.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): Rediscover_0.3.3.tgz, r-oldrel (x86_64): Rediscover_0.3.3.tgz
Old sources:	Rediscover archive

Linking:

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