Package: CREAM 1.1.1

Benjamin Haibe-Kains

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.

Authors:Seyed Ali Madani Tonekaboni [aut], Victor Kofia [aut], Mathieu Lupien [aut], Benjamin Haibe-Kains [aut, cre]

CREAM_1.1.1.tar.gz
CREAM_1.1.1.zip(r-4.5)CREAM_1.1.1.zip(r-4.4)CREAM_1.1.1.zip(r-4.3)
CREAM_1.1.1.tgz(r-4.4-any)CREAM_1.1.1.tgz(r-4.3-any)
CREAM_1.1.1.tar.gz(r-4.5-noble)CREAM_1.1.1.tar.gz(r-4.4-noble)
CREAM_1.1.1.tgz(r-4.4-emscripten)CREAM_1.1.1.tgz(r-4.3-emscripten)
CREAM.pdf |CREAM.html✨
CREAM/json (API)

Peer review:

Bug tracker:https://github.com/bhklab/cream/issues

On CRAN:

peakdetectionfunctionalpredictionbiomedicalinformaticsclusteringbiomedical-informaticsfunctional-predictionpeak-detection

5 exports 12 stars 3.39 score 0 dependencies 16 mentions 15 scripts 182 downloads

Last updated 4 years agofrom:718264747f. Checks:OK: 1 ERROR: 6. Indexed: yes.

Exports:CREAMElementRecogPeakMinFiltWindowSizeRecogWindowVec

Dependencies: