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CREAM  

Clustering of Genomic Regions Analysis Method
View on CRAN: Click here


Download and install CREAM package within the R console
Install from CRAN:
install.packages("CREAM")

Install from Github:
library("remotes")
install_github("cran/CREAM")

Install by package version:
library("remotes")
install_version("CREAM", "1.1.1")



Attach the package and use:
library("CREAM")
Maintained by
Benjamin Haibe-Kains
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-10-27
Latest Update: 2018-06-06
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.
How to cite:
Benjamin Haibe-Kains (2017). CREAM: Clustering of Genomic Regions Analysis Method. R package version 1.1.1, https://cran.r-project.org/web/packages/CREAM
Previous versions and publish date:
1.0.0 (2017-10-27 10:19), 1.1.0 (2018-01-05 17:05)
Other packages that cited CREAM R package
View CREAM citation profile
Other R packages that CREAM depends, imports, suggests or enhances
Functions, R codes and Examples using the CREAM R package
Some associated functions: CREAM . ElementRecog . PeakMinFilt . WindowSizeRecog . WindowVec . 
Some associated R codes: CREAM.R . ElementRecog.R . PeakMinFilt.R . WindowSizeRecog.R . WindowVec.R .  Full CREAM package functions and examples
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