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CREAM
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]
[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. Accessed 21 Nov. 2024.
Other packages that cited CREAM R package
View CREAM citation profile
Other R packages that CREAM depends,
imports, suggests or enhances
Complete documentation for CREAM
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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