Package: muRtools 0.9.6

Fabian Mueller

muRtools: Mueller's R tools

Fabian's custom plotting functions and utilities

Authors:Fabian Mueller

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'))

Peer review:

Bug tracker:https://github.com/demuellae/murtools/issues

On CRAN:

115 exports 1 stars 0.23 score 46 dependencies

Last updated 11 months agofrom:f19bda1707

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 pageTopics
aggregateDfaggregateDf
bed2GRangesbed2GRanges
bedTobigBedbedTobigBed
camel2underscorecamel2underscore
chordDiagramFromContingencyTablechordDiagramFromContingencyTable
col.text.2.hexcol.text.2.hex
colorize.valuecolorize.value
Custom Color Paletescolpal,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.contcolpal.cont
Custom Color Paletes for epigenetic modificationscolgrad.methylation.rb colgrad.methylation.yb colpal.histone colpal.histone,colpal.histone.ihec,colgrad.methylation.rb,colgrad.methylation.yb colpal.histone.ihec
combinationListcombinationList
Methods for recognizing histone modifications from stringscontainsHistoneModStr containsHistoneModStr,getHistoneFromHistoneModStr,getAaPosFromHistoneModStr,getModFromHistoneModStr,matchHistoneModStr getAaPosFromHistoneModStr getAaTypeFromHistoneModStr getHistoneFromHistoneModStr getModFromHistoneModStr matchHistoneModStr normalizeHistoneModStr
countPairwiseOverlapscountPairwiseOverlaps
create.densityScattercreate.densityScatter
densRanksdensRanks
df2grangesdf2granges
diagDivCellHeatmapdiagDivCellHeatmap
diagDivHeatmapdiagDivHeatmap
dist.correlationdist.correlation
downloadLolaDbsdownloadLolaDbs
get.encode.cell.tableget.encode.cell.table
getAnnotGrl.gencodegetAnnotGrl.gencode
getAssocTestRes.pcagetAssocTestRes.pca
getCellTypesFromLolaDbgetCellTypesFromLolaDb
getClusteringDendrogramgetClusteringDendrogram
getColorFungetColorFun
getConfiggetConfig
getDimRedCoords.mdsgetDimRedCoords.mds
getDimRedCoords.pcagetDimRedCoords.pca
getDimRedCoords.tsnegetDimRedCoords.tsne
getDimRedCoords.umapgetDimRedCoords.umap
getDimRedPlotgetDimRedPlot
getGeneAnnotMapgetGeneAnnotMap
getGenomeGrgetGenomeGr
getGenomeObjectgetGenomeObject
getHashStringgetHashString
getNamesFromLolaDbgetNamesFromLolaDb
getPointDensitygetPointDensity
getRegionSetgetRegionSet
getRelatedAnaDirFromConfiggetRelatedAnaDirFromConfig
getSeqlengths4assemblygetSeqlengths4assembly
getTargetFromLolaDbgetTargetFromLolaDb
getTilingRegionsgetTilingRegions
getTxDb.gencodegetTxDb.gencode
ggAutoColorScaleggAutoColorScale
ggMessagePlotggMessagePlot
ggplot2.distrggplot2.distr
ggplot2.heatmapggplot2.heatmap
ggsave4docggsave4doc
ggtempggtemp
goEnrichmentgoEnrichment
granges2bedgranges2bed
granges2bed.igvgranges2bed.igv
granges2igvgranges2igv
grGeneAnnotgrGeneAnnot
grLiftOvergrLiftOver
grSignedDistancegrSignedDistance
grTilegrTile
indicesInListindicesInList
kde.plotkde.plot kde.plot.matrix kde.plot.simple
loadLolaDbsloadLolaDbs
loadRnBeadsAnalysisloadRnBeadsAnalysis
lolaBarPlotlolaBarPlot
lolaBoxPlotPerTargetlolaBoxPlotPerTarget
lolaRegionSetHeatmap Plot a heatmap in which the rows are different user sets and the color corresponds to an enrichment scorelolaRegionSetHeatmap
lolaVolcanoPlotlolaVolcanoPlot
makeTransmakeTrans
matchStrandmatchStrand
muRtools: Mueller's R toolsmuRtools
normalize.strnormalize.str
normalizePercentilenormalizePercentile
normalizeRanknormalizeRank
pairsDensCorpairsDensCor
panel.cor.colpanel.cor.col
panel.densitypanel.density
parse.cl.argsparse.cl.args
parse.encode.cv.fileparse.encode.cv.file
pdftemppdftemp
plotAllDimRedplotAllDimRed
plotColpalplotColpal
plotCorPhmplotCorPhm
getDimRedPlotplotDimRed
plotFisherTestplotFisherTest
pngtemppngtemp
randomGroupedHeatmaprandomGroupedHeatmap
readTabreadTab
reloadPackagereloadPackage
rowTtestrowTtest
runLOLA_list More robust version of lola for lists of user sets (to avoid "Negative c entry in table" errors)runLOLA_list
scatter.twogroupsscatter.twogroups
setGenomePropssetGenomeProps
sortGrsortGr
strTrimstrTrim
summarizeSetOverlapsummarizeSetOverlap
testAssoctestAssoc
textSearchtextSearch
theme_nogridtheme_nogrid
umapParamGridReportumapParamGridReport
underscore2camelunderscore2camel
unloadPackageunloadPackage
writeTabwriteTab