Package: nearBynding
Type: Package
Title: Discern RNA structure proximal to protein binding
Version: 1.20.0
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, Seqinfo,
        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
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:02:17 UTC
RemoteUrl: https://github.com/bioc/nearBynding
RemoteRef: RELEASE_3_22
RemoteSha: a5f36da38d86570e2fc94893481c8bc288d833c3
NeedsCompilation: no
Packaged: 2025-11-11 16:14:09 UTC; root
Author: Veronica Busa [cre]
Maintainer: Veronica Busa <vbusa1@jhmi.edu>
Built: R 4.5.2; ; 2025-11-11 16:24:50 UTC; windows
