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
