RBPSpecificity
This is the development version of RBPSpecificity; to use it, please install the devel version of Bioconductor.
RBP Inherent Specificity and Variation Sensitivity Analysis Tool
Bioconductor version: Development (3.24)
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).
Author: Soon Yi [aut, cre]
, National Institutes of Health [fnd] (T32 GM152319)
Maintainer: Soon Yi <cu.soonyi at gmail.com>
citation("RBPSpecificity")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("RBPSpecificity")
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("RBPSpecificity")| Introduction to RBPSpecificity | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, GeneRegulation, GenomeAnnotation, KEGG, MotifAnnotation, Sequencing, Software, Visualization |
| Version | 0.99.6 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.6.0) |
| Imports | Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, ggplot2, methods, reshape2, S4Vectors, stats, utils |
| System Requirements | |
| 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 |
See More
| Suggests | BiocStyle, BSgenome.Hsapiens.UCSC.hg38, IRanges, knitr, rmarkdown, testthat |
| 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 | RBPSpecificity_0.99.6.tar.gz |
| Windows Binary (x86_64) | RBPSpecificity_0.99.6.zip |
| macOS Binary (big-sur-x86_64) | RBPSpecificity_0.99.6.tgz |
| macOS Binary (sonoma-arm64) | RBPSpecificity_0.99.6.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RBPSpecificity |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RBPSpecificity |
| Bioc Package Browser | https://code.bioconductor.org/browse/RBPSpecificity/ |
| Package Short Url | https://bioconductor.org/packages/RBPSpecificity/ |
| Package Downloads Report | Download Stats |