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CREAM (Clustering of genomic REgions Analysis Method)

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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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