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Bioconductor - BindingSiteFinder

BindingSiteFinder

This is the released version of BindingSiteFinder; for the devel version, see BindingSiteFinder.

Binding site defintion based on iCLIP data

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-1778-0248 , Melina Klostermann [aut] ORCID: 0000-0003-3122-1095 , Kathi Zarnack [aut] ORCID: 0000-0003-3527-3378

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

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

To install this package, start R (version "4.5") 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")
Details biocViews Coverage, DataImport, FunctionalGenomics, GeneExpression, GeneRegulation, Sequencing, Software Version 2.6.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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, txdbmaker, ggrepel, stringr Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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