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("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 | ||
| 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 | |
| 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_1.6.0.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 |