BindingSiteFinder

DOI: 10.18129/B9.bioc.BindingSiteFinder  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see BindingSiteFinder.

Binding site defintion based on iCLIP data

Bioconductor version: 3.17

Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

Author: Mirko Brüggemann [aut, cre] , Kathi Zarnack [aut]

Maintainer: Mirko Brüggemann <mirko.brueggemann at mail.de>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("BindingSiteFinder")

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("BindingSiteFinder")

 

HTML	R Script	Definition of binding sites from iCLIP signal
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DataImport, FunctionalGenomics, GeneExpression, GeneRegulation, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	Artistic-2.0
Depends	GenomicRanges, R (>= 4.2)
Imports	tidyr, tibble, dplyr, plyr, matrixStats, stats, ggplot2, methods, rtracklayer, S4Vectors, ggforce, GenomeInfoDb, Gviz
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, ComplexHeatmap, forcats, scales
SystemRequirements
Enhances
URL
BugReports	https://github.com/ZarnackGroup/BindingSiteFinder/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BindingSiteFinder_1.6.0.tar.gz
Windows Binary	BindingSiteFinder_1.6.0.zip
macOS Binary (x86_64)	BindingSiteFinder_1.6.0.tgz
macOS Binary (arm64)	BindingSiteFinder_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BindingSiteFinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BindingSiteFinder
Bioc Package Browser	https://code.bioconductor.org/browse/BindingSiteFinder/
Package Short Url	https://bioconductor.org/packages/BindingSiteFinder/
Package Downloads Report	Download Stats