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: 1.1.1
Depends: R (≥ 3.3)
Imports: stats, utils
Suggests: testthat
Published: 2018-06-06
DOI: 10.32614/CRAN.package.CREAM
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>
License: GPL (≥ 3)
NeedsCompilation: no
Materials: README
CRAN checks: CREAM results


Reference manual: CREAM.pdf


Package source: CREAM_1.1.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): CREAM_1.1.1.tgz, r-oldrel (arm64): CREAM_1.1.1.tgz, r-release (x86_64): CREAM_1.1.1.tgz, r-oldrel (x86_64): CREAM_1.1.1.tgz
Old sources: CREAM archive


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