nearBynding

DOI: 10.18129/B9.bioc.nearBynding  

Discern RNA structure proximal to protein binding

Bioconductor version: Release (3.16)

Provides a pipeline to discern RNA structure at and proximal to the site of protein binding within regions of the transcriptome defined by the user. CLIP protein-binding data can be input as either aligned BAM or peak-called bedGraph files. RNA structure can either be predicted internally from sequence or users have the option to input their own RNA structure data. RNA structure binding profiles can be visually and quantitatively compared across multiple formats.

Author: Veronica Busa [cre]

Maintainer: Veronica Busa <vbusa1 at jhmi.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("nearBynding")

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("nearBynding")

 

PDF	R Script	nearBynding Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DataRepresentation, MotifDiscovery, MultipleComparison, Software, StructuralPrediction, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	Artistic-2.0
Depends	R (>= 4.0)
Imports	R.utils, matrixStats, plyranges, transport, Rsamtools, S4Vectors, grDevices, graphics, rtracklayer, dplyr, GenomeInfoDb, methods, GenomicRanges, utils, stats, magrittr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots, BiocGenerics, rlang
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements	bedtools (>= 2.28.0), Stereogene (>= v2.22), CapR (>= 1.1.1)
Enhances
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Depends On Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	nearBynding_1.8.0.tar.gz
Windows Binary	nearBynding_1.8.0.zip
macOS Binary (x86_64)	nearBynding_1.8.0.tgz
macOS Binary (arm64)	nearBynding_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/nearBynding
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/nearBynding
Bioc Package Browser	https://code.bioconductor.org/browse/nearBynding/
Package Short Url	https://bioconductor.org/packages/nearBynding/
Package Downloads Report	Download Stats