nearBynding

DOI: 10.18129/B9.bioc.nearBynding    

This is the development version of nearBynding; for the stable release version, see nearBynding.

Discern RNA structure proximal to protein binding

Bioconductor version: Development (3.13)

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>

Citation (from within R, enter citation("nearBynding")):

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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
SystemRequirements bedtools (>= 2.28.0), Stereogene (>= v2.20), CapR (>= 1.1.1)
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package nearBynding_1.1.0.tar.gz
Windows Binary nearBynding_1.1.0.zip
macOS 10.13 (High Sierra) nearBynding_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/nearBynding
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/nearBynding
Package Short Url https://bioconductor.org/packages/nearBynding/
Package Downloads Report Download Stats

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