BindingSiteFinder

DOI: 10.18129/B9.bioc.BindingSiteFinder    

Binding site defintion based on iCLIP data

Bioconductor version: Release (3.14)

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 Br├╝ggemann [aut, cre] , Kathi Zarnack [aut]

Maintainer: Mirko Br├╝ggemann <mirko.brueggemann at mail.de>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
License Artistic-2.0
Depends GenomicRanges, R (>= 4.1)
Imports tidyr, matrixStats, stats, ggplot2, methods, rtracklayer, S4Vectors, ggforce
LinkingTo
Suggests testthat, BiocStyle, knitr, rmarkdown, dplyr, GenomicAlignments, ComplexHeatmap, GenomeInfoDb, 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_1.0.0.tar.gz
Windows Binary BindingSiteFinder_1.0.0.zip
macOS 10.13 (High Sierra) BindingSiteFinder_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BindingSiteFinder
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BindingSiteFinder
Package Short Url https://bioconductor.org/packages/BindingSiteFinder/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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