The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
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 (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 |
Please use the canonical form https://CRAN.R-project.org/package=CREAM to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.