fcScan
fcScan for detecting clusters of coordinates with user defined options
Bioconductor version: Release (3.19)
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("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 | ||
NEWS | Text |
Details
biocViews | Clustering, GenomeAnnotation, Software |
Version | 1.18.0 |
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 |
See More
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_1.18.0.tar.gz |
Windows Binary | fcScan_1.18.0.zip |
macOS Binary (x86_64) | fcScan_1.18.0.tgz |
macOS Binary (arm64) | fcScan_1.18.0.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 |