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fcScan

fcScan for detecting clusters of coordinates with user defined options


Bioconductor version: Release (3.18)

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: Abdullah El-Kurdi [aut], Ghiwa khalil [aut], Georges Khazen [ctb], Pierre Khoueiry [aut, cre]

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

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
fcScan HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, GenomeAnnotation, Software
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License Artistic-2.0
Depends
Imports stats, plyr, VariantAnnotation, SummarizedExperiment, rtracklayer, GenomicRanges, methods, IRanges, foreach, doParallel, parallel
System Requirements
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Suggests RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
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Package Archives

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

Source Package fcScan_1.16.0.tar.gz
Windows Binary fcScan_1.16.0.zip
macOS Binary (x86_64) fcScan_1.16.0.tgz
macOS Binary (arm64) fcScan_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/fcScan
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/fcScan
Bioc Package Browser https://code.bioconductor.org/browse/fcScan/
Package Short Url https://bioconductor.org/packages/fcScan/
Package Downloads Report Download Stats