Man pages for demuellae/muRtools
Mueller's R tools
| aggregateDf | aggregateDf |
| bed2GRanges | bed2GRanges |
| bedTobigBed | bedTobigBed |
| camel2underscore | camel2underscore |
| chordDiagramFromContingencyTable | chordDiagramFromContingencyTable |
| colorize.value | colorize.value |
| colpal | Custom Color Paletes |
| colpal.cont | colpal.cont |
| colpal.epigenetics | Custom Color Paletes for epigenetic modifications |
| col.text.2.hex | col.text.2.hex |
| combinationList | combinationList |
| countPairwiseOverlaps | countPairwiseOverlaps |
| create.densityScatter | create.densityScatter |
| densRanks | densRanks |
| df2granges | df2granges |
| diagDivCellHeatmap | diagDivCellHeatmap |
| diagDivHeatmap | diagDivHeatmap |
| dist.correlation | dist.correlation |
| downloadLolaDbs | downloadLolaDbs |
| 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 |
| get.encode.cell.table | get.encode.cell.table |
| 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 |
| HistoneModStr | Methods for recognizing histone modifications from strings |
| indicesInList | indicesInList |
| kde.plot | kde.plot |
| loadLolaDbs | loadLolaDbs |
| loadRnBeadsAnalysis | loadRnBeadsAnalysis |
| lolaBarPlot | lolaBarPlot |
| lolaBoxPlotPerTarget | lolaBoxPlotPerTarget |
| lolaRegionSetHeatmap | lolaRegionSetHeatmap Plot a heatmap in which the rows are... |
| lolaVolcanoPlot | lolaVolcanoPlot |
| makeTrans | makeTrans |
| matchStrand | matchStrand |
| muRtools | muRtools: Mueller's R tools |
| normalizePercentile | normalizePercentile |
| normalizeRank | normalizeRank |
| normalize.str | normalize.str |
| 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 |
| plotDimRed | getDimRedPlot |
| plotFisherTest | plotFisherTest |
| pngtemp | pngtemp |
| randomGroupedHeatmap | randomGroupedHeatmap |
| readTab | readTab |
| reloadPackage | reloadPackage |
| rowTtest | rowTtest |
| runLOLA_list | runLOLA_list More robust version of lola for lists of user... |
| 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 |
