nearBynding
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see nearBynding.
Discern RNA structure proximal to protein binding
Bioconductor version: 3.14
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("nearBynding")):
Installation
To install this package, start R (version "4.1") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DataRepresentation, MotifDiscovery, MultipleComparison, Software, StructuralPrediction, Visualization |
| Version | 1.4.0 |
| 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) |
| URL |
See More
| Suggests | knitr, rmarkdown |
| 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 | nearBynding_1.4.0.tar.gz |
| Windows Binary | nearBynding_1.4.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | nearBynding_1.4.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |