Package: muRtools 0.9.6
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 |