The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

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: 0.3.2
Depends: R (≥ 4.0), Matrix, PoissonBinomial, ShiftConvolvePoibin, utils, matrixStats
Imports: maftools, data.table, parallel, RColorBrewer, methods
Suggests: knitr, rmarkdown, RUnit, BiocStyle, BiocGenerics, dplyr, kableExtra, magick, stats, qvalue
Published: 2023-04-14
DOI: 10.32614/CRAN.package.Rediscover
Author: Juan A. Ferrer-Bonsoms, Laura Jareno, and Angel Rubio
Maintainer: Juan A. Ferrer-Bonsoms <jafhernandez at tecnun.es>
License: Artistic-2.0
NeedsCompilation: no
Citation: Rediscover citation info
Materials: README NEWS
In views: Omics
CRAN checks: Rediscover results

Documentation:

Reference manual: Rediscover.pdf
Vignettes: Rediscover

Downloads:

Package source: Rediscover_0.3.2.tar.gz
Windows binaries: r-devel: Rediscover_0.3.2.zip, r-release: Rediscover_0.3.2.zip, r-oldrel: Rediscover_0.3.2.zip
macOS binaries: r-release (arm64): Rediscover_0.3.2.tgz, r-oldrel (arm64): Rediscover_0.3.2.tgz, r-release (x86_64): Rediscover_0.3.2.tgz, r-oldrel (x86_64): Rediscover_0.3.2.tgz
Old sources: Rediscover archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=Rediscover to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.