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

Discern RNA structure proximal to protein binding

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

nearBynding Vignette PDF R Script
Reference Manual PDF


biocViews Clustering, DataRepresentation, MotifDiscovery, MultipleComparison, Software, StructuralPrediction, Visualization
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
System Requirements bedtools (>= 2.28.0), Stereogene (>= v2.22), CapR (>= 1.1.1)
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Source Package nearBynding_1.15.0.tar.gz
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