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BindingSiteFinder

Binding site defintion based on iCLIP data


Bioconductor version: Release (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 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 "4.3") 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")
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 2.0.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
System Requirements
URL
Bug Reports https://github.com/ZarnackGroup/BindingSiteFinder/issues
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr
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Package Archives

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

Source Package BindingSiteFinder_2.0.0.tar.gz
Windows Binary BindingSiteFinder_2.0.0.zip
macOS Binary (x86_64) BindingSiteFinder_2.0.0.tgz
macOS Binary (arm64) BindingSiteFinder_2.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BindingSiteFinder
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BindingSiteFinder
Bioc Package Browser https://code.bioconductor.org/browse/BindingSiteFinder/
Package Short Url https://bioconductor.org/packages/BindingSiteFinder/
Package Downloads Report Download Stats