fcScan

DOI: 10.18129/B9.bioc.fcScan    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see fcScan.

fcScan for detecting clusters of coordinates with user defined options

Bioconductor version: 3.10

This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a "greedy" option allowing thus the presence of additional sites within the allowed window size.

Author: Abdallah El-Kurdi <ak161 at aub.edu.lb> Ghiwa khalil <gk39 at aub.edu.lb> Georges Khazen <gkhazen at lau.edu.lb> Pierre Khoueiry <pk17 at aub.edu.lb>

Maintainer: Pierre Khoueiry <pk17 at aub.edu.lb> Abdallah El-Kurdi <ak161 at aub.edu.lb>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("fcScan")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("fcScan")

 

HTML	R Script	fcScan
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, GenomeAnnotation, Software
Version	1.0.0
In Bioconductor since	BioC 3.10 (R-3.6) (< 6 months)
License	Artistic-2.0
Depends
Imports	stats, plyr, VariantAnnotation, SummarizedExperiment, rtracklayer, GenomicRanges, methods, IRanges
LinkingTo
Suggests	RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	fcScan_1.0.0.tar.gz
Windows Binary	fcScan_1.0.0.zip
Mac OS X 10.11 (El Capitan)	fcScan_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/fcScan
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/fcScan
Package Short Url	https://bioconductor.org/packages/fcScan/
Package Downloads Report	Download Stats