CAGExploreR: Analyzes Differential Promoter Composition in CAGE data

CAGExploreR implements an algorithm to calculate and evaluate the statistical significance of the uncertainty coefficient (a.k.a. Theil's U or the proportional entropy reduction). This statistic measures the strength of association between two nominal random variables. One specific application of this package is the detection of differential composition (differences in vectors of proportions) of genes subunits (e.g. promoters) across various biological conditions. The two nominal variables here are the biological conditions and the promoters within genes. The differential composition and the genomic location of these promoters can also be visualized using this package.

Version: 1.0.2
Depends: R (≥ 3.0.2), edgeR, data.table, AnnotationDbi
Imports: rbamtools, R2HTML, GenomicFeatures, biomaRt
Suggests: knitr
Published: 2014-02-09
Author: Emmanuel Dimont
Maintainer: Emmanuel Dimont <edimont at mail.harvard.edu>
BugReports: https://github.com/edimont/CAGExploreR/issues
License: MIT + file LICENSE
URL: https://github.com/edimont/CAGExploreR
NeedsCompilation: no
Materials: README
CRAN checks: CAGExploreR results

Downloads:

Reference manual: CAGExploreR.pdf
Vignettes: CAGExploreR Manual
Package source: CAGExploreR_1.0.2.tar.gz
OS X binary: not available, see check log.
Windows binary: CAGExploreR_1.0.2.zip
Old sources: CAGExploreR archive