RBPSpecificity

RBP Inherent Specificity and Variation Sensitivity Analysis Tool

Bioconductor version: 3.24 · Package version: 0.99.6

Provides tools to analyze RNA Binding Protein (RBP) binding specificities from high-throughput sequencing data. Functions include calculating K-mer enrichment, Inherent Specificity (IS), and Mutational Sensitivity (VS), along with visualization of IS and VS. For detailed methodology and applications, please refer to our manuscript (see URL field or vignette).

DOI: 10.18129/B9.bioc.RBPSpecificity

Installation

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

BiocManager::install("RBPSpecificity")

Details

Maintainer	Soon Yi <cu.soonyi@gmail.com>
Author	Soon Yi [aut, cre] (ORCID: <https://orcid.org/0000-0002-4535-6532>), National Institutes of Health [fnd] (T32 GM152319)
License	GPL-3
URL	https://www.biorxiv.org/content/10.1101/2025.03.28.646018v2, https://github.com/S00NYI/RBPSpecificity, https://github.com/S00NYI/BITS_Specificity
Bug Reports	https://github.com/S00NYI/RBPSpecificity/issues
Source branch	devel
Build report	Bioconductor build system, r-universe
biocViews	Coverage, GeneRegulation, GenomeAnnotation, KEGG, MotifAnnotation, Sequencing, Software, Visualization
Package Short Url	https://bioconductor.org/packages/RBPSpecificity/

Citation

From within R, enter citation("RBPSpecificity"):

Soon Yi. RBPSpecificity: RBP Inherent Specificity and Variation Sensitivity Analysis Tool. doi:10.18129/B9.bioc.RBPSpecificity, R package version 0.99.6, https://bioconductor.org/packages/RBPSpecificity.

Generated from the package metadata; it may differ from the package's own citation.

Documentation

Introduction to RBPSpecificity

Download

Follow the installation instructions to use this package in your R session.

Source package	RBPSpecificity_0.99.6.tar.gz
Windows binary (x86_64)	RBPSpecificity_0.99.6.zip
macOS binary (arm64)	RBPSpecificity_0.99.6.tgz
macOS binary (x86_64)	RBPSpecificity_0.99.6.tgz

Dependencies

Depends: R (>= 4.5.0)

Imports: Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, ggplot2, methods, reshape2, S4Vectors, stats, utils

Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, IRanges, knitr, rmarkdown, testthat