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: 0.3.0
Depends: R (≥ 4.0), Matrix, speedglm, PoissonBinomial, ShiftConvolvePoibin, utils, matrixStats
Imports: maftools, data.table, parallel, RColorBrewer, methods
Suggests: knitr, rmarkdown, RUnit, BiocStyle, BiocGenerics, dplyr, kableExtra, TCGAbiolinks, magick, stats, qvalue
Published: 2021-10-06
Author: Juan A. Ferrer-Bonsoms Developer [aut, cre], Laura Jareno Developer [aut], Angel Rubio User [aut, ctb]
Maintainer: Juan A. Ferrer-Bonsoms Developer <jafhernandez at tecnun.es>
License: Artistic-2.0
NeedsCompilation: no
Citation: Rediscover citation info
Materials: README NEWS
CRAN checks: Rediscover results

Downloads:

Reference manual: Rediscover.pdf
Vignettes: Rediscover
Package source: Rediscover_0.3.0.tar.gz
Windows binaries: r-devel: Rediscover_0.3.0.zip, r-release: Rediscover_0.3.0.zip, r-oldrel: Rediscover_0.2.0.zip
macOS binaries: r-release (arm64): Rediscover_0.2.0.tgz, r-release (x86_64): not available, r-oldrel: not available
Old sources: Rediscover archive

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