Site2Target
This is the development version of Site2Target; to use it, please install the devel version of Bioconductor.
An R package to associate peaks and target genes
Bioconductor version: Development (3.21)
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")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | 0.99.5 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| 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_0.99.5.tar.gz |
| Windows Binary (x86_64) | Site2Target_0.99.5.zip |
| macOS Binary (x86_64) | Site2Target_0.99.5.tgz |
| macOS Binary (arm64) | Site2Target_0.99.5.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 |