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 |
| 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: | GPL (≥ 3) |
| URL: | https://github.com/bhklab/CREAM |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | CREAM results |
| Reference manual: | CREAM.pdf |
| Package source: | CREAM_1.1.1.tar.gz |
| Windows binaries: | r-devel: CREAM_1.1.1.zip, r-release: CREAM_1.1.1.zip, r-oldrel: CREAM_1.1.1.zip |
| macOS binaries: | r-release: CREAM_1.1.1.tgz, r-oldrel: CREAM_1.1.1.tgz |
| Old sources: | CREAM archive |
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