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BindingSiteFinder

Binding site defintion based on iCLIP data

Bioconductor version: 3.23 · Package version: 2.10.0

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.

Installation

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

BiocManager::install("BindingSiteFinder")

Details

MaintainerMirko Brüggemann <mirko.brueggemann@mail.de>
AuthorMirko Brüggemann [aut, cre] (ORCID: <https://orcid.org/0000-0002-1778-0248>), Melina Klostermann [aut] (ORCID: <https://orcid.org/0000-0003-3122-1095>), Kathi Zarnack [aut] (ORCID: <https://orcid.org/0000-0003-3527-3378>)
LicenseArtistic-2.0
Bug Reportshttps://github.com/ZarnackGroup/BindingSiteFinder/issues
Downloads rank299
Source branchRELEASE_3_23
biocViewsCoverage, DataImport, FunctionalGenomics, GeneExpression, GeneRegulation, Sequencing, Software

Documentation

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Dependencies

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

Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr, txdbmaker, ggrepel, stringr