CRAN/E | CREAM

CREAM

Clustering of Genomic Regions Analysis Method

Installation

About

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.

github.com/bhklab/CREAM
Bug report File report

Key Metrics

Version 1.1.1
R ≥ 3.3
Published 2018-06-06 2145 days ago
Needs compilation? no
License GPL (≥ 3)
CRAN checks CREAM results

Downloads

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Maintainer

Maintainer

Benjamin Haibe-Kains

benjamin.haibe.kains@utoronto.ca

Authors

Seyed Ali Madani Tonekaboni

aut

Victor Kofia

aut

Mathieu Lupien

aut

Benjamin Haibe-Kains

aut / cre

Material

README
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

CREAM archive

Depends

R ≥ 3.3

Imports

stats
utils

Suggests

testthat