https://github.com/bhklab/CREAM

CREAM (Clustering of Functional Regions Analysis Method) is a new method for identification of clusters of functional regions (COREs) within chromosomes.
https://github.com/bhklab/CREAM

biomedical-informatics clustering functional-prediction peak-detection

Last synced: 3 months ago
JSON representation

CREAM (Clustering of Functional Regions Analysis Method) is a new method for identification of clusters of functional regions (COREs) within chromosomes.

• Host: GitHub
• URL: https://github.com/bhklab/CREAM
• Owner: bhklab
• Created: 2017-07-12T14:00:38.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2021-02-11T01:54:32.000Z (almost 4 years ago)
• Last Synced: 2024-11-08T00:32:29.864Z (3 months ago)
• Topics: biomedical-informatics, clustering, functional-prediction, peak-detection
• Language: R
• Homepage:
• Size: 2.47 MB
• Stars: 12
• Watchers: 5
• Forks: 3
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• AwesomeGenomics - CREAM

README

        
# CREAM (Clustering of genomic REgions Analysis Method) #

[![Travis Build Status](https://travis-ci.org/bhklab/CREAM.svg?branch=master)](https://travis-ci.org/bhklab/CREAM) [![codecov](https://codecov.io/gh/bhklab/CREAM/branch/master/graph/badge.svg)](https://codecov.io/gh/bhklab/CREAM) [![AppVeyor Build status](https://ci.appveyor.com/api/projects/status/gvxbin36u3yqx50s?svg=true)](https://ci.appveyor.com/project/kofiav/cream-l3j9o) [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version-last-release/CREAM)](https://cran.r-project.org/package=CREAM)  [![CRAN\_Downloads](https://cranlogs.r-pkg.org/badges/CREAM)](https://cran.r-project.org/package=CREAM)

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

------------

``` r

# Install from CRAN

install.packages('CREAM')

# Installing the development version from GitHub:

# install.packages("devtools")

devtools::install_github("bhklab/CREAM")

```

Usage

-----

``` r

# 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](https://github.com/bhklab/CREAM/issues) page.