fcScan
This is the released version of fcScan; for the devel version, see fcScan.
fcScan for detecting clusters of coordinates with user defined options
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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_1.26.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | fcScan_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | fcScan_1.26.0.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 |