Site2Target

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see Site2Target.

An R package to associate peaks and target genes

Bioconductor version: 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] ORCID iD ORCID: 0000-0003-4820-4101

Maintainer: Peyman Zarrineh <peyman.zarrineh at manchester.ac.uk>

Citation (from within R, enter citation("Site2Target")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, ChIPSeq, Epigenetics, GeneExpression, GeneTarget, Software

Version 1.0.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 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

Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

Imports Me

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Site2Target_1.0.0.tar.gz

Windows Binary (x86_64) Site2Target_1.0.0.zip (64-bit only)

macOS Binary (x86_64) Site2Target_1.0.0.tgz

macOS Binary (arm64) Site2Target_1.0.0.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/

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