fcScan

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see fcScan.

fcScan for detecting clusters of coordinates with user defined options


Bioconductor version: 3.13

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 <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> Abdullah El-Kurdi <ak161 at aub.edu.lb>

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

Installation

To install this package, start R (version "4.1") 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 1.6.0
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
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_1.6.0.tar.gz
Windows Binary fcScan_1.6.0.zip
macOS 10.13 (High Sierra) fcScan_1.6.0.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
Old Source Packages for BioC 3.13 Source Archive