BindingSiteFinder
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see BindingSiteFinder.
Binding site defintion based on iCLIP data
Bioconductor version: 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("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 | ||
| 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 |
| 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.
| 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 |