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:Jonathan Price [aut, cre], Andrew Lim [ctb]

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'))

Peer review:

Bug tracker:https://github.com/jlp-bioinf/rnacrosslinkoo/issues

On CRAN:

comradespsoralenrna-crosslinkingrna-structurerna-structure-prediction

5.43 score 1 stars 3 scripts 168 downloads 40 exports 153 dependencies

Last updated 11 days agofrom:336afbfa9f. Checks:OK: 6 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxWARNINGNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:clusterGrangesListclusterGrangesList<-clusterNumbersclusterrnaCrosslinkclusterTableFoldedclusterTableListclusterTableList<-compareKnowncompareKnownStructuresfeatureInfofoldrnaCrosslinkgetDatagetInteractionsgetReverseInteractionsgroupInputFilesmakeExamplernaCrosslinkDataSetmatrixListmatrixList<-plotClusterAgreementplotClusterAgreementHeatplotCombinedMatrixplotComparisonArcplotEnsemblePCAplotInteractionsplotInteractionsAverageplotMatricesplotMatricesAverageplotStructurereadNumbersrnaCrosslinkDataSetrnaCrosslinkQCrnasrnaSizesampleNamessampleTabletopInteracterstopInteractionstopTranscriptstrimClusters

Dependencies:ade4askpassbackportsbase64encBiobaseBiocGenericsBiostringsbitbit64blobbroombslibcachemcallrcellrangerClassDiscoveryclicliprclustercodetoolscolorspaceconflictedcpp11crayoncrosstalkcurldata.tableDBIdbplyrdigestdoParalleldplyrdtplyrevaluatefansifarverfastclusterfastmapfontawesomeforcatsforeachfsgarglegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegoogledrivegooglesheets4gtablehavenheatmap3highrhmshtmltoolshtmlwidgetshttridsigraphIRangesisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmatrixStatsmclustmemoisemgcvmimemixtoolsmodelrmunsellnlmeoompaBaseoompaDataopensslpatchworkpillarpixmappkgconfigplotlyplyrprettyunitsprocessxprogresspromisespspurrrR4RNAR6raggrappdirsRColorBrewerRcppRcppArmadilloreadrreadxlrematchrematch2reprexreshape2rlangrmarkdownRRNArstudioapirvestS4VectorssassscalessegmentedselectrseqinrspstringistringrsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetinytexTopDomtzdbUCSC.utilsutf8uuidvctrsviridisLitevroomwithrxfunxml2XVectoryamlzlibbioc

rnaCrosslinkOO

Jonathan Price

Rendered fromrnaCrosslinkOO.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-07-10
Started: 2024-02-18

Readme and manuals

Help Manual

Help pageTopics
clusterGrangesListclusterGrangesList clusterGrangesList,rnaCrosslinkDataSet-method
clusterGrangesList<-clusterGrangesList<- clusterGrangesList<-,rnaCrosslinkDataSet-method
clusterNumbersclusterNumbers clusterNumbers,rnaCrosslinkDataSet-method
clusterrnaCrosslinkclusterrnaCrosslink clusterrnaCrosslink,rnaCrosslinkDataSet-method
clusterTableFoldedclusterTableFolded clusterTableFolded,rnaCrosslinkDataSet-method
clusterTableListclusterTableList clusterTableList,rnaCrosslinkDataSet-method
clusterTableList<-clusterTableList<- clusterTableList<-,rnaCrosslinkDataSet-method
compareKnowncompareKnown compareKnown,rnaCrosslinkDataSet-method
compareKnownStructurescompareKnownStructures compareKnownStructures,rnaCrosslinkDataSet-method
featureInfofeatureInfo featureInfo,rnaCrosslinkDataSet-method
findBasePairsRNAcoFold2findBasePairsRNAcoFold2
findBasePairsRNAfoldfindBasePairsRNAfold
findBasePairsRNAfold2findBasePairsRNAfold2
foldrnaCrosslinkfoldrnaCrosslink foldrnaCrosslink,rnaCrosslinkDataSet-method
getAdjacancyMatgetAdjacancyMat
getClusterClusterShortRangeWholegetClusterClusterShortRangeWhole
getDatagetData getData,rnaCrosslinkDataSet-method
getInteractionsgetInteractions getInteractions,rnaCrosslinkDataSet-method
getMatricesgetMatrices
getReverseInteractionsgetReverseInteractions getReverseInteractions,rnaCrosslinkDataSet-method
groupgroup group,rnaCrosslinkDataSet-method
InputFilesInputFiles InputFiles,rnaCrosslinkDataSet-method
InputToGRangesInputToGRanges
makeExamplernaCrosslinkDataSetmakeExamplernaCrosslinkDataSet
matrixListmatrixList matrixList,rnaCrosslinkDataSet-method
matrixListmatrixList<- matrixList<-,rnaCrosslinkDataSet-method
Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performedplotClusterAgreement plotClusterAgreement,rnaCrosslinkDataSet-method
Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performedplotClusterAgreementHeat 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 mapplotCombinedMatrix plotCombinedMatrix,rnaCrosslinkDataSet-method
plotComparisonArcplotComparisonArc plotComparisonArc,rnaCrosslinkDataSet-method
plotEnsemblePCAplotEnsemblePCA plotEnsemblePCA,rnaCrosslinkDataSet-method
Plots a contact map of interactions of each sample of an RNA (interactor) on the RNA of interestplotInteractions plotInteractions,rnaCrosslinkDataSet-method
Plots a contact map of interactions of all samples of an RNA (interactor) on the RNA of interestplotInteractionsAverage plotInteractionsAverage,rnaCrosslinkDataSet-method
Plots a number of contact maps to file of each sample for a stage in the analysisplotMatrices plotMatrices,rnaCrosslinkDataSet-method
plotMatricesAverageplotMatricesAverage plotMatricesAverage,rnaCrosslinkDataSet-method
plotStructureplotStructure plotStructure,rnaCrosslinkDataSet-method
printClustersFastprintClustersFast
readNumbersreadNumbers readNumbers,rnaCrosslinkDataSet-method
rnaCrosslinkDataSetrnaCrosslinkDataSet rnaCrosslinkDataSet-class
rnaCrosslinkQCrnaCrosslinkQC
rnasrnas rnas,rnaCrosslinkDataSet-method
rnaSizernaSize rnaSize,rnaCrosslinkDataSet-method
sampleChimerassampleChimeras
sampleNamessampleNames sampleNames,rnaCrosslinkDataSet-method
sampleTablesampleTable sampleTable,rnaCrosslinkDataSet-method
subsetInputList2subsetInputList2
swapInputsswapInputs
swapInputs2swapInputs2
swapInputs3swapInputs3
topInteracterstopInteracters topInteracters,rnaCrosslinkDataSet-method
topInteractionstopInteractions topInteractions,rnaCrosslinkDataSet-method
topTranscriptstopTranscripts topTranscripts,rnaCrosslinkDataSet-method
trimClusterstrimClusters trimClusters,rnaCrosslinkDataSet-method