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nearBynding

Discern RNA structure proximal to protein binding

Bioconductor version: Release (3.17)

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 "4.3") 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")
nearBynding Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, DataRepresentation, MotifDiscovery, MultipleComparison, Software, StructuralPrediction, Visualization
Version 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 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
Linking To
Suggests knitr, rmarkdown
System Requirements bedtools (>= 2.28.0), Stereogene (>= v2.22), CapR (>= 1.1.1)
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Package Archives

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

Source Package nearBynding_1.10.0.tar.gz
Windows Binary nearBynding_1.10.0.zip
macOS Binary (x86_64) nearBynding_1.10.0.tgz
macOS Binary (arm64) nearBynding_1.10.0.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/
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