CREAM: Clustering of Genomic Regions Analysis Method

Provides a new method for identification of clusters of genomic regions within chromosomes. Primarily, it is used for calling clusters of cis-regulatory elements (COREs). 'CREAM' uses genome-wide maps of genomic regions in the tissue or cell type of interest, such as those generated from chromatin-based assays including DNaseI, ATAC or ChIP-Seq. 'CREAM' considers proximity of the elements within chromosomes of a given sample to identify COREs in the following steps: 1) It identifies window size or the maximum allowed distance between the elements within each CORE, 2) It identifies number of elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which does not pass the threshold considered in the approach.

Version: 1.0.0
Depends: R (≥ 3.3)
Imports: stats, utils
Suggests: testthat
Published: 2017-10-27
Author: Seyed Ali Madani Tonekaboni [aut], Victor Kofia [aut], Mathieu Lupien [aut], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>
BugReports: https://github.com/bhklab/CREAM/issues
License: Artistic-2.0
URL: https://github.com/bhklab/CREAM
NeedsCompilation: no
Materials: README
CRAN checks: CREAM results

Downloads:

Reference manual: CREAM.pdf
Package source: CREAM_1.0.0.tar.gz
Windows binaries: r-devel: CREAM_1.0.0.zip, r-release: CREAM_1.0.0.zip, r-oldrel: CREAM_1.0.0.zip
OS X El Capitan binaries: r-release: CREAM_1.0.0.tgz
OS X Mavericks binaries: r-oldrel: CREAM_1.0.0.tgz

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