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.

Getting started

Package details

AuthorSeyed Ali Madani Tonekaboni [aut], Victor Kofia [aut], Mathieu Lupien [aut], Benjamin Haibe-Kains [aut, cre]
Bioconductor views BiomedicalInformatics Clustering FunctionalPrediction PeakDetection
MaintainerBenjamin Haibe-Kains <[email protected]>
LicenseGPL (>= 3)
Version1.1.1
URL https://github.com/bhklab/CREAM
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("CREAM")

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CREAM documentation built on May 2, 2019, 6:57 a.m.