Repository files navigation

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.

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

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

Contact us by filing an issue in the CREAMissues page.