Package: rnaCrosslinkOO 0.1.4
rnaCrosslinkOO: Analysis of RNA Crosslinking Data
Analysis of RNA crosslinking data for RNA structure prediction. The package is suitable for the analysis of RNA structure cross-linking data and chemical probing data.
Authors:
rnaCrosslinkOO_0.1.4.tar.gz
rnaCrosslinkOO_0.1.4.zip(r-4.5)rnaCrosslinkOO_0.1.4.zip(r-4.4)rnaCrosslinkOO_0.1.4.zip(r-4.3)
rnaCrosslinkOO_0.1.4.tgz(r-4.4-any)rnaCrosslinkOO_0.1.4.tgz(r-4.3-any)
rnaCrosslinkOO_0.1.4.tar.gz(r-4.5-noble)rnaCrosslinkOO_0.1.4.tar.gz(r-4.4-noble)
rnaCrosslinkOO_0.1.4.tgz(r-4.4-emscripten)rnaCrosslinkOO_0.1.4.tgz(r-4.3-emscripten)
rnaCrosslinkOO.pdf |rnaCrosslinkOO.html✨
rnaCrosslinkOO/json (API)
| # Install 'rnaCrosslinkOO' in R: |
| install.packages('rnaCrosslinkOO', repos = c('https://jlp-bioinf.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jlp-bioinf/rnacrosslinkoo/issues
comradespsoralenrna-crosslinkingrna-structurerna-structure-prediction
Last updated 1 months agofrom:44cbe8213b. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 08 2024 |
| R-4.5-win | OK | Sep 08 2024 |
| R-4.5-linux | OK | Sep 08 2024 |
| R-4.4-win | OK | Sep 08 2024 |
| R-4.4-mac | OK | Sep 08 2024 |
| R-4.3-win | OK | Sep 08 2024 |
| R-4.3-mac | OK | Sep 08 2024 |
Exports:clusterGrangesListclusterGrangesList<-clusterNumbersclusterrnaCrosslinkclusterTableFoldedclusterTableListclusterTableList<-compareKnowncompareKnownStructuresfeatureInfofoldrnaCrosslinkgetDatagetInteractionsgetReverseInteractionsgroupInputFilesmakeExamplernaCrosslinkDataSetmatrixListmatrixList<-plotClusterAgreementplotClusterAgreementHeatplotCombinedMatrixplotComparisonArcplotEnsemblePCAplotInteractionsplotInteractionsAverageplotMatricesplotMatricesAverageplotStructurereadNumbersrnaCrosslinkDataSetrnaCrosslinkQCrnasrnaSizesampleNamessampleTabletopInteracterstopInteractionstopTranscriptstrimClusters
Dependencies:ade4askpassbackportsbase64encBiobaseBiocGenericsBiostringsbitbit64blobbroombslibcachemcallrcellrangerClassDiscoveryclicliprclustercodetoolscolorspaceconflictedcpp11crayoncrosstalkcurldata.tableDBIdbplyrdigestdoParalleldplyrdtplyrevaluatefansifarverfastclusterfastmapfontawesomeforcatsforeachfsgarglegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegoogledrivegooglesheets4gtablehavenheatmap3highrhmshtmltoolshtmlwidgetshttridsigraphIRangesisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmatrixStatsmclustmemoisemgcvmimemixtoolsmodelrmunsellnlmeoompaBaseoompaDataopensslpatchworkpillarpixmappkgconfigplotlyplyrprettyunitsprocessxprogresspromisespspurrrR4RNAR6raggrappdirsRColorBrewerRcppRcppArmadilloreadrreadxlrematchrematch2reprexreshape2rlangrmarkdownRRNArstudioapirvestS4VectorssassscalessegmentedselectrseqinrspstringistringrsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetinytexTopDomtzdbUCSC.utilsutf8uuidvctrsviridisLitevroomwithrxfunxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| clusterGrangesList | clusterGrangesList clusterGrangesList,rnaCrosslinkDataSet-method |
| clusterGrangesList<- | clusterGrangesList<- clusterGrangesList<-,rnaCrosslinkDataSet-method |
| clusterNumbers | clusterNumbers clusterNumbers,rnaCrosslinkDataSet-method |
| clusterrnaCrosslink | clusterrnaCrosslink clusterrnaCrosslink,rnaCrosslinkDataSet-method |
| clusterTableFolded | clusterTableFolded clusterTableFolded,rnaCrosslinkDataSet-method |
| clusterTableList | clusterTableList clusterTableList,rnaCrosslinkDataSet-method |
| clusterTableList<- | clusterTableList<- clusterTableList<-,rnaCrosslinkDataSet-method |
| compareKnown | compareKnown compareKnown,rnaCrosslinkDataSet-method |
| compareKnownStructures | compareKnownStructures compareKnownStructures,rnaCrosslinkDataSet-method |
| featureInfo | featureInfo featureInfo,rnaCrosslinkDataSet-method |
| findBasePairsRNAcoFold2 | findBasePairsRNAcoFold2 |
| findBasePairsRNAfold | findBasePairsRNAfold |
| findBasePairsRNAfold2 | findBasePairsRNAfold2 |
| foldrnaCrosslink | foldrnaCrosslink foldrnaCrosslink,rnaCrosslinkDataSet-method |
| getAdjacancyMat | getAdjacancyMat |
| getClusterClusterShortRangeWhole | getClusterClusterShortRangeWhole |
| getData | getData getData,rnaCrosslinkDataSet-method |
| getInteractions | getInteractions getInteractions,rnaCrosslinkDataSet-method |
| getMatrices | getMatrices |
| getReverseInteractions | getReverseInteractions getReverseInteractions,rnaCrosslinkDataSet-method |
| group | group group,rnaCrosslinkDataSet-method |
| InputFiles | InputFiles InputFiles,rnaCrosslinkDataSet-method |
| InputToGRanges | InputToGRanges |
| makeExamplernaCrosslinkDataSet | makeExamplernaCrosslinkDataSet |
| matrixList | matrixList matrixList,rnaCrosslinkDataSet-method |
| matrixList | matrixList<- matrixList<-,rnaCrosslinkDataSet-method |
| Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performed | plotClusterAgreement plotClusterAgreement,rnaCrosslinkDataSet-method |
| Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performed | plotClusterAgreementHeat plotClusterAgreementHeat,rnaCrosslinkDataSet-method |
| Plots a contact map of two chosen samples for chosen stages in the analysis, with each chosen sample on separate halves of the contact map | plotCombinedMatrix plotCombinedMatrix,rnaCrosslinkDataSet-method |
| plotComparisonArc | plotComparisonArc plotComparisonArc,rnaCrosslinkDataSet-method |
| plotEnsemblePCA | plotEnsemblePCA plotEnsemblePCA,rnaCrosslinkDataSet-method |
| Plots a contact map of interactions of each sample of an RNA (interactor) on the RNA of interest | plotInteractions plotInteractions,rnaCrosslinkDataSet-method |
| Plots a contact map of interactions of all samples of an RNA (interactor) on the RNA of interest | plotInteractionsAverage plotInteractionsAverage,rnaCrosslinkDataSet-method |
| Plots a number of contact maps to file of each sample for a stage in the analysis | plotMatrices plotMatrices,rnaCrosslinkDataSet-method |
| plotMatricesAverage | plotMatricesAverage plotMatricesAverage,rnaCrosslinkDataSet-method |
| plotStructure | plotStructure plotStructure,rnaCrosslinkDataSet-method |
| printClustersFast | printClustersFast |
| readNumbers | readNumbers readNumbers,rnaCrosslinkDataSet-method |
| rnaCrosslinkDataSet | rnaCrosslinkDataSet rnaCrosslinkDataSet-class |
| rnaCrosslinkQC | rnaCrosslinkQC |
| rnas | rnas rnas,rnaCrosslinkDataSet-method |
| rnaSize | rnaSize rnaSize,rnaCrosslinkDataSet-method |
| sampleChimeras | sampleChimeras |
| sampleNames | sampleNames sampleNames,rnaCrosslinkDataSet-method |
| sampleTable | sampleTable sampleTable,rnaCrosslinkDataSet-method |
| subsetInputList2 | subsetInputList2 |
| swapInputs | swapInputs |
| swapInputs2 | swapInputs2 |
| swapInputs3 | swapInputs3 |
| topInteracters | topInteracters topInteracters,rnaCrosslinkDataSet-method |
| topInteractions | topInteractions topInteractions,rnaCrosslinkDataSet-method |
| topTranscripts | topTranscripts topTranscripts,rnaCrosslinkDataSet-method |
| trimClusters | trimClusters trimClusters,rnaCrosslinkDataSet-method |
