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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).

Installation

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

BiocManager::install("RBPSpecificity")

Details

MaintainerSoon Yi <cu.soonyi@gmail.com>
AuthorSoon Yi [aut, cre] (ORCID: <https://orcid.org/0000-0002-4535-6532>), National Institutes of Health [fnd] (T32 GM152319)
LicenseGPL-3
URLhttps://www.biorxiv.org/content/10.1101/2025.03.28.646018v2, https://github.com/S00NYI/RBPSpecificity, https://github.com/S00NYI/BITS_Specificity
Bug Reportshttps://github.com/S00NYI/RBPSpecificity/issues
Downloads rank47
Source branchdevel
biocViewsCoverage, GeneRegulation, GenomeAnnotation, KEGG, MotifAnnotation, Sequencing, Software, Visualization

Documentation

Download

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

Source packageRBPSpecificity_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