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.


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Overview

CREAM is 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.

Installation

# Install from CRAN
install.packages('CREAM')
 
# Installing the development version from GitHub:
# install.packages("devtools")
devtools::install_github("bhklab/CREAM")

Usage

# Identify COREs using CREAM
IdentifiedCOREs <- CREAM( in_path = system.file("extdata", "A549_Chr21.bed", package = "CREAM"), MinLength = 1000, peakNumMin = 2 )

Getting help

Contact us by filing an issue in the CREAM issues page.

News

Reference manual

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install.packages("CREAM")

1.1.1 by Benjamin Haibe-Kains, 8 months ago


https://github.com/bhklab/CREAM


Report a bug at https://github.com/bhklab/CREAM/issues


Browse source code at https://github.com/cran/CREAM


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


Documentation:   PDF Manual  


GPL (>= 3) license


Imports stats, utils

Suggests testthat


See at CRAN