Package: CREAM
Type: Package
Title: Clustering of Genomic Regions Analysis Method
Version: 1.1.1
Date: 2018-05-30
Authors@R: c(
    person("Seyed Ali", "Madani Tonekaboni", , email = "ali.madanitonekaboni@mail.utoronto.ca", role = c("aut")),
    person("Victor", "Kofia", , email = "victor.kofia@uhnresearch.ca", role = c("aut")),
    person("Mathieu", "Lupien", , email = "mlupien@uhnres.utoronto.ca", role = c("aut")),
    person("Benjamin", "Haibe-Kains", , email = "benjamin.haibe.kains@utoronto.ca", role = c("aut", "cre"))
    )
Description: 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.
License: GPL (>= 3)
Imports: stats, utils
Depends: R (>= 3.3)
URL: https://github.com/bhklab/CREAM
Suggests: testthat
RoxygenNote: 6.0.1
Roxygen: list(markdown = TRUE)
LazyData: true
biocViews: PeakDetection, FunctionalPrediction, BiomedicalInformatics,
        Clustering
BugReports: https://github.com/bhklab/CREAM/issues
Encoding: UTF-8
Repository: https://bhklab.r-universe.dev
Date/Publication: 2021-02-11 01:54:32 UTC
RemoteUrl: https://github.com/bhklab/cream
RemoteRef: HEAD
RemoteSha: 718264747fd4f6886ffcfc260d70fb2b2892b04d
NeedsCompilation: no
Packaged: 2026-06-15 11:18:06 UTC; root
Author: Seyed Ali Madani Tonekaboni [aut],
  Victor Kofia [aut],
  Mathieu Lupien [aut],
  Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>