Package: nearBynding 1.17.0
Veronica Busa
nearBynding: Discern RNA structure proximal to protein binding
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.
Authors:
nearBynding_1.17.0.tar.gz
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nearBynding_1.17.0.tgz(r-4.4-any)nearBynding_1.17.0.tgz(r-4.3-any)
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nearBynding.pdf |nearBynding.html✨
nearBynding/json (API)
NEWS
| # Install 'nearBynding' in R: |
| install.packages('nearBynding', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:nearBynding-1.15.0(bioc 3.20)nearBynding-1.14.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
visualizationmotifdiscoverydatarepresentationstructuralpredictionclusteringmultiplecomparison
Last updated 23 days agofrom:287e346731. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | OK | Oct 31 2024 |
| R-4.5-linux | OK | Oct 30 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:assessGroupingbindingContextDistancebindingContextDistanceCapRCleanBAMtoBGCleanBEDtoBGExtractTranscriptomeSequenceGenomeMappingToChainFileget_outfilesgetChainChrSizeliftOverToExomicBGprocessCapRoutrunCapRrunStereogenerunStereogeneOnCapRsymmetryCapRsymmetryContextvisualizeCapRStereogenevisualizeStereogenewrite_configwrite_fasta
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcaToolsclicodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydplyrfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegplotsgtablegtoolshttrIRangesisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrangespngR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbletidyselecttransportTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGeneUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| assessGrouping | assessGrouping |
| bindingContextDistance | bindingContextDistance |
| bindingContextDistanceCapR | bindingContextDistanceCapR |
| CleanBAMtoBG | CleanBAMtoBG |
| CleanBEDtoBG | CleanBEDtoBG |
| ExtractTranscriptomeSequence | ExtractTranscriptomeSequence |
| GenomeMappingToChainFile | GenomeMappingToChainFile |
| get_outfiles | get_outfiles |
| getChainChrSize | getChainChrSize |
| liftOverToExomicBG | liftOverToExomicBG |
| Discern RNA structure proximal to protein binding | nearBynding-package nearBynding |
| processCapRout | processCapRout |
| runCapR | runCapR |
| runStereogene | runStereogene |
| runStereogeneOnCapR | runStereogeneOnCapR |
| symmetryCapR | symmetryCapR |
| symmetryContext | symmetryContext |
| visualizeCapRStereogene | visualizeCapRStereogene |
| visualizeStereogene | visualizeStereogene |
| write_config | write_config |
| write_fasta | write_fasta |