Site2Target
This is the development version of Site2Target; for the stable release version, see Site2Target.
An R package to associate peaks and target genes
Bioconductor version: Development (3.24)
Statistics implemented for both peak-wise and gene-wise associations. In peak-wise associations, the p-value of the target genes of a given set of peaks are calculated. Negative binomial or Poisson distributions can be used for modeling the unweighted peaks targets and log-nromal can be used to model the weighted peaks. In gene-wise associations a table consisting of a set of genes, mapped to specific peaks, is generated using the given rules.
Author: Peyman Zarrineh [cre, aut]
Maintainer: Peyman Zarrineh <peyman.zarrineh at manchester.ac.uk>
citation("Site2Target")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("Site2Target")
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("Site2Target")| Site2Target | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, ChIPSeq, Epigenetics, GeneExpression, GeneTarget, Software |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.4) |
| Imports | S4Vectors, stats, utils, BiocGenerics, GenomeInfoDb, MASS, IRanges, GenomicRanges |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/fls-bioinformatics-core/Site2Target/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| 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 | Site2Target_1.5.0.tar.gz |
| Windows Binary (x86_64) | Site2Target_1.5.0.zip |
| macOS Binary (big-sur-x86_64) | Site2Target_1.5.0.tgz |
| macOS Binary (sonoma-arm64) | Site2Target_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Site2Target |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Site2Target |
| Bioc Package Browser | https://code.bioconductor.org/browse/Site2Target/ |
| Package Short Url | https://bioconductor.org/packages/Site2Target/ |
| Package Downloads Report | Download Stats |