fcScan

DOI: 10.18129/B9.bioc.fcScan    

fcScan for detecting clusters of coordinates with user defined options

Bioconductor version: Release (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>

Citation (from within R, enter citation("fcScan")):

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: