fcScan

fcScan for detecting clusters of coordinates with user defined options

Bioconductor version: Release (3.20)

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, GenomeAnnotation, Software
Version	1.20.0
In Bioconductor since	BioC 3.10 (R-3.6) (5 years)
License	Artistic-2.0
Depends
Imports	stats, plyr, VariantAnnotation, SummarizedExperiment, rtracklayer, GenomicRanges, methods, IRanges, foreach, doParallel, parallel
System Requirements
URL

Suggests	RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	fcScan_1.20.0.tar.gz
Windows Binary (x86_64)	fcScan_1.20.0.zip (64-bit only)
macOS Binary (x86_64)	fcScan_1.20.0.tgz
macOS Binary (arm64)	fcScan_1.19.0.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