Calculates cryptic scores for genes using the ratio (Cheung et al., 2008), the 3' enrichment method (DeGennaro et al., 2013) and the probabilistic method. It also provide methods to estimates cryptic transcription start sites.

Documentation

Manual: yCrypticRNAs.pdf
Vignette: yCrypticRNAs

Maintainer: Nicole Uwimana <nicole.uwimana at gmail.com>

Author(s): Nicole Uwimana, Benjamin Haibe-Kains, Francois Robert

Install package and any missing dependencies by running this line in your R console:

install.packages("yCrypticRNAs")

Depends R (>= 3.2.0)
Imports biomaRt (>= 2.24.1), data.table(>=1.9.6), IRanges (>= 2.2.9), mclust(>=5.1), MESS(>=0.3-2), parallel (>= 3.2.2), Rcpp(>=0.12.1), Rsamtools(>= 1.20.5)
Suggests knitr, testthat, rmarkdown
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Package yCrypticRNAs
Materials
URL https://bitbucket.org/nuwimana/ycrypticrnas
Task Views
Version 0.99.2
Published 2016-02-08
License GPL-2
BugReports https://bitbucket.org/nuwimana/ycrypticrnas/issues
SystemRequirements
NeedsCompilation yes
Citation
CRAN checks yCrypticRNAs check results
Package source yCrypticRNAs_0.99.2.tar.gz