This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

BindingSiteFinder

This is the development version of BindingSiteFinder; for the stable release version, see BindingSiteFinder.

Binding site defintion based on iCLIP data

Bioconductor version: Development (3.18)

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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Coverage, DataImport, FunctionalGenomics, GeneExpression, GeneRegulation, Sequencing, Software
Version 1.7.4
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License Artistic-2.0
Depends GenomicRanges, R (>= 4.2)
Imports tidyr, tibble, plyr, matrixStats, stats, ggplot2, methods, rtracklayer, S4Vectors, ggforce, GenomeInfoDb, ComplexHeatmap, RColorBrewer, lifecycle, rlang, forcats, dplyr, GenomicFeatures, IRanges, kableExtra, ggdist
Linking To
Suggests testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify
System Requirements
Enhances
URL
Bug Reports https://github.com/ZarnackGroup/BindingSiteFinder/issues
See More
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_1.7.4.tar.gz
Windows Binary BindingSiteFinder_1.7.4.zip
macOS Binary (x86_64) BindingSiteFinder_1.7.4.tgz
macOS Binary (arm64) BindingSiteFinder_1.7.3.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