Package: nearBynding
Type: Package
Title: Discern RNA structure proximal to protein binding
Version: 1.18.0
Authors@R: person("Veronica", "Busa", email="vbusa1@jhmi.edu", role=c("cre"))
Description: 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.
License: Artistic-2.0
biocViews: Visualization, MotifDiscovery, DataRepresentation,
        StructuralPrediction, Clustering, MultipleComparison
Encoding: UTF-8
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
Suggests: knitr, rmarkdown
SystemRequirements: bedtools (>= 2.28.0), Stereogene (>= v2.22), CapR
        (>= 1.1.1)
VignetteBuilder: knitr
Collate: 'assessGrouping.R' 'bindingContextDistance.R'
        'bindingContextDistanceCapR.R' 'CleanBAMtoBG.R'
        'CleanBEDtoBG.R' 'ExtractTranscriptomeSequence.R'
        'GenomeMappingToChainFile.R' 'get_outfiles.R'
        'liftOverToExomicBG.R' 'processCapRout.R' 'runCapR.R'
        'runStereogene.R' 'runStereogeneOnCapR.R'
        'visualizeCapRStereogene.R' 'visualizeStereogene.R'
        'write_config.R' 'write_fasta.R' 'getChainChrSize.R'
        'utilities.R' 'symmetryCapR.R' 'symmetryContext.R'
RoxygenNote: 7.1.1
git_url: https://git.bioconductor.org/packages/nearBynding
git_branch: RELEASE_3_21
git_last_commit: 98fc873
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 02:24:10 UTC; biocbuild
Author: Veronica Busa [cre]
Maintainer: Veronica Busa <vbusa1@jhmi.edu>
Built: R 4.5.0; ; 2025-04-16 15:01:56 UTC; windows
