Package: muRtools 0.9.6
Fabian Mueller
muRtools: Mueller's R tools
Fabian's custom plotting functions and utilities
Authors:
muRtools_0.9.6.tar.gz
muRtools_0.9.6.zip(r-4.5)muRtools_0.9.6.zip(r-4.4)muRtools_0.9.6.zip(r-4.3)
muRtools_0.9.6.tgz(r-4.4-any)muRtools_0.9.6.tgz(r-4.3-any)
muRtools_0.9.6.tar.gz(r-4.5-noble)muRtools_0.9.6.tar.gz(r-4.4-noble)
muRtools_0.9.6.tgz(r-4.4-emscripten)muRtools_0.9.6.tgz(r-4.3-emscripten)
muRtools.pdf |muRtools.html✨
muRtools/json (API)
| # Install 'muRtools' in R: |
| install.packages('muRtools', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/demuellae/murtools/issues
Last updated 1 years agofrom:f19bda1707. Checks:OK: 1 ERROR: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 26 2024 |
| R-4.5-win | ERROR | Aug 26 2024 |
| R-4.5-linux | ERROR | Aug 26 2024 |
| R-4.4-win | ERROR | Aug 26 2024 |
| R-4.4-mac | ERROR | Aug 26 2024 |
| R-4.3-win | ERROR | Aug 26 2024 |
| R-4.3-mac | ERROR | Aug 26 2024 |
Exports:aggregateDfbed2GRangescamel2underscorechordDiagramFromContingencyTablecol.text.2.hexcolgrad.methylation.rbcolgrad.methylation.ybcolorize.valuecolpal.bdecolpal.cbcolpal.contcolpal.corpidcolpal.histonecolpal.histone.iheccolpal.iwh.cb01colpal.miniblazecolpal.mu.catcolpal.naturecolpal.PhFr.acolpal.solarextracolpals.gamescolpals.topocombinationListcontainsHistoneModStrcountPairwiseOverlapscreate.densityScatterdf2grangesdiagDivCellHeatmapdiagDivHeatmapdist.correlationdownloadLolaDbsget.encode.cell.tablegetAaPosFromHistoneModStrgetAaTypeFromHistoneModStrgetAnnotGrl.gencodegetAssocTestRes.pcagetCellTypesFromLolaDbgetClusteringDendrogramgetColorFungetConfiggetDimRedCoords.mdsgetDimRedCoords.pcagetDimRedCoords.tsnegetDimRedCoords.umapgetDimRedPlotgetGeneAnnotMapgetGenomeGrgetGenomeObjectgetHashStringgetHistoneFromHistoneModStrgetModFromHistoneModStrgetNamesFromLolaDbgetPointDensitygetRegionSetgetRelatedAnaDirFromConfiggetSeqlengths4assemblygetTargetFromLolaDbgetTilingRegionsgetTxDb.gencodeggAutoColorScaleggMessagePlotggplot2.distrggplot2.heatmapggsave4docggtempgoEnrichmentgranges2bedgranges2bed.igvgranges2igvgrGeneAnnotgrLiftOvergrSignedDistancegrTileindicesInListkde.plot.matrixkde.plot.simpleloadLolaDbsloadRnBeadsAnalysislolaBarPlotlolaBoxPlotPerTargetlolaRegionSetHeatmaplolaVolcanoPlotmakeTransmatchHistoneModStrnormalize.strnormalizeHistoneModStrnormalizePercentilenormalizeRankpairsDensCorparse.cl.argsparse.encode.cv.filepdftempplotAllDimRedplotColpalplotCorPhmplotDimRedplotFisherTestpngtemprandomGroupedHeatmapreadTabreloadPackagerowTtestrunLOLA_listscatter.twogroupssetGenomePropssortGrstrTrimsummarizeSetOverlaptestAssoctextSearchtheme_nogridumapParamGridReportunderscore2camelunloadPackagewriteTab
Dependencies:askpassBiocGenericsclicolorspacecurldata.tablefansifarverGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemuLogRmunsellnlmeopensslpillarpkgconfigR6RColorBrewerrlangS4VectorsscalessystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| aggregateDf | aggregateDf |
| bed2GRanges | bed2GRanges |
| bedTobigBed | bedTobigBed |
| camel2underscore | camel2underscore |
| chordDiagramFromContingencyTable | chordDiagramFromContingencyTable |
| col.text.2.hex | col.text.2.hex |
| colorize.value | colorize.value |
| Custom Color Paletes | colpal,colpal.cb,colpal.colpal.bde colpal.bde colpal.cb colpal.corpid colpal.iwh.cb01 colpal.miniblaze colpal.mu.cat colpal.nature colpal.PhFr.a colpal.solarextra colpals.games colpals.topo |
| colpal.cont | colpal.cont |
| Custom Color Paletes for epigenetic modifications | colgrad.methylation.rb colgrad.methylation.yb colpal.histone colpal.histone,colpal.histone.ihec,colgrad.methylation.rb,colgrad.methylation.yb colpal.histone.ihec |
| combinationList | combinationList |
| Methods for recognizing histone modifications from strings | containsHistoneModStr containsHistoneModStr,getHistoneFromHistoneModStr,getAaPosFromHistoneModStr,getModFromHistoneModStr,matchHistoneModStr getAaPosFromHistoneModStr getAaTypeFromHistoneModStr getHistoneFromHistoneModStr getModFromHistoneModStr matchHistoneModStr normalizeHistoneModStr |
| countPairwiseOverlaps | countPairwiseOverlaps |
| create.densityScatter | create.densityScatter |
| densRanks | densRanks |
| df2granges | df2granges |
| diagDivCellHeatmap | diagDivCellHeatmap |
| diagDivHeatmap | diagDivHeatmap |
| dist.correlation | dist.correlation |
| downloadLolaDbs | downloadLolaDbs |
| get.encode.cell.table | get.encode.cell.table |
| getAnnotGrl.gencode | getAnnotGrl.gencode |
| getAssocTestRes.pca | getAssocTestRes.pca |
| getCellTypesFromLolaDb | getCellTypesFromLolaDb |
| getClusteringDendrogram | getClusteringDendrogram |
| getColorFun | getColorFun |
| getConfig | getConfig |
| getDimRedCoords.mds | getDimRedCoords.mds |
| getDimRedCoords.pca | getDimRedCoords.pca |
| getDimRedCoords.tsne | getDimRedCoords.tsne |
| getDimRedCoords.umap | getDimRedCoords.umap |
| getDimRedPlot | getDimRedPlot |
| getGeneAnnotMap | getGeneAnnotMap |
| getGenomeGr | getGenomeGr |
| getGenomeObject | getGenomeObject |
| getHashString | getHashString |
| getNamesFromLolaDb | getNamesFromLolaDb |
| getPointDensity | getPointDensity |
| getRegionSet | getRegionSet |
| getRelatedAnaDirFromConfig | getRelatedAnaDirFromConfig |
| getSeqlengths4assembly | getSeqlengths4assembly |
| getTargetFromLolaDb | getTargetFromLolaDb |
| getTilingRegions | getTilingRegions |
| getTxDb.gencode | getTxDb.gencode |
| ggAutoColorScale | ggAutoColorScale |
| ggMessagePlot | ggMessagePlot |
| ggplot2.distr | ggplot2.distr |
| ggplot2.heatmap | ggplot2.heatmap |
| ggsave4doc | ggsave4doc |
| ggtemp | ggtemp |
| goEnrichment | goEnrichment |
| granges2bed | granges2bed |
| granges2bed.igv | granges2bed.igv |
| granges2igv | granges2igv |
| grGeneAnnot | grGeneAnnot |
| grLiftOver | grLiftOver |
| grSignedDistance | grSignedDistance |
| grTile | grTile |
| indicesInList | indicesInList |
| kde.plot | kde.plot kde.plot.matrix kde.plot.simple |
| loadLolaDbs | loadLolaDbs |
| loadRnBeadsAnalysis | loadRnBeadsAnalysis |
| lolaBarPlot | lolaBarPlot |
| lolaBoxPlotPerTarget | lolaBoxPlotPerTarget |
| lolaRegionSetHeatmap Plot a heatmap in which the rows are different user sets and the color corresponds to an enrichment score | lolaRegionSetHeatmap |
| lolaVolcanoPlot | lolaVolcanoPlot |
| makeTrans | makeTrans |
| matchStrand | matchStrand |
| muRtools: Mueller's R tools | muRtools |
| normalize.str | normalize.str |
| normalizePercentile | normalizePercentile |
| normalizeRank | normalizeRank |
| pairsDensCor | pairsDensCor |
| panel.cor.col | panel.cor.col |
| panel.density | panel.density |
| parse.cl.args | parse.cl.args |
| parse.encode.cv.file | parse.encode.cv.file |
| pdftemp | pdftemp |
| plotAllDimRed | plotAllDimRed |
| plotColpal | plotColpal |
| plotCorPhm | plotCorPhm |
| getDimRedPlot | plotDimRed |
| plotFisherTest | plotFisherTest |
| pngtemp | pngtemp |
| randomGroupedHeatmap | randomGroupedHeatmap |
| readTab | readTab |
| reloadPackage | reloadPackage |
| rowTtest | rowTtest |
| runLOLA_list More robust version of lola for lists of user sets (to avoid "Negative c entry in table" errors) | runLOLA_list |
| scatter.twogroups | scatter.twogroups |
| setGenomeProps | setGenomeProps |
| sortGr | sortGr |
| strTrim | strTrim |
| summarizeSetOverlap | summarizeSetOverlap |
| testAssoc | testAssoc |
| textSearch | textSearch |
| theme_nogrid | theme_nogrid |
| umapParamGridReport | umapParamGridReport |
| underscore2camel | underscore2camel |
| unloadPackage | unloadPackage |
| writeTab | writeTab |
