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
| Maintainer | Mirko Brüggemann <mirko.brueggemann@mail.de> |
| Author | Mirko 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>) |
| License | Artistic-2.0 |
| Bug Reports | https://github.com/ZarnackGroup/BindingSiteFinder/issues |
| Downloads rank | 299 |
| Source branch | RELEASE_3_23 |
| biocViews | Coverage, DataImport, FunctionalGenomics, GeneExpression, GeneRegulation, Sequencing, Software |
Documentation
Download
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