Files in Albluca/rpgraph
r interface to VDAOEngine to build elastic principal graphs
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R/LoadData.R
R/Web.R
R/_DevelopPckg.R
R/conversions.R
R/dashboards.R
R/expression.R
R/filtering.R
R/graphs.R
R/pca.r
R/pipelines.R
R/plotting.R
R/principal_graphs.R
R/projections.R
R/staging.R
R/utilities.R
R/zzz.R
README.Rmd
README.md
data/HumanGenes_GOCellCycle.rda
data/HumanGenes_GODNAReplication.rda
data/MouseENS_KowaCellCycle.rda
data/MouseGenes_GOCellCycle.rda
data/MouseGenes_GODNAReplication.rda
data/MouseGenes_KowaCellCycle.rda
data/StageAssociation_Whit.rda
data/StageAssociation_Whit_Coarse.rda
data/StageAssociation_Whit_Coarse_G0.rda
data/StageAssociation_Whit_Ext.rda
data/StageAssociation_Whit_G0.rda
data/simple_circle.rda
data/simple_iris.rda
data/simple_tree.rda
doc/circle.Rmd
doc/circle.md
doc/circle_files/figure-markdown_github/unnamed-chunk-10-1.png
doc/circle_files/figure-markdown_github/unnamed-chunk-11-1.png
doc/circle_files/figure-markdown_github/unnamed-chunk-12-1.png
doc/circle_files/figure-markdown_github/unnamed-chunk-2-1.png
doc/circle_files/figure-markdown_github/unnamed-chunk-3-1.png
doc/circle_files/figure-markdown_github/unnamed-chunk-4-1.png
doc/circle_files/figure-markdown_github/unnamed-chunk-5-1.png
doc/circle_files/figure-markdown_github/unnamed-chunk-7-1.png
doc/circle_files/figure-markdown_github/unnamed-chunk-8-1.png
doc/curve.Rmd
doc/curve.md
doc/curve_files/figure-markdown_github/unnamed-chunk-12-1.png
doc/curve_files/figure-markdown_github/unnamed-chunk-2-1.png
doc/curve_files/figure-markdown_github/unnamed-chunk-3-1.png
doc/curve_files/figure-markdown_github/unnamed-chunk-4-1.png
doc/curve_files/figure-markdown_github/unnamed-chunk-5-1.png
doc/curve_files/figure-markdown_github/unnamed-chunk-7-1.png
doc/curve_files/figure-markdown_github/unnamed-chunk-8-1.png
doc/javapar.Rmd
doc/javapar.md
doc/javapar_files/figure-markdown_github/unnamed-chunk-2-1.png
doc/javapar_files/figure-markdown_github/unnamed-chunk-4-1.png
doc/javapar_files/figure-markdown_github/unnamed-chunk-6-1.png
doc/javapar_files/figure-markdown_github/unnamed-chunk-8-1.png
doc/mix.Rmd
doc/mix.md
doc/mix_files/figure-markdown_github/unnamed-chunk-11-1.png
doc/mix_files/figure-markdown_github/unnamed-chunk-13-1.png
doc/mix_files/figure-markdown_github/unnamed-chunk-2-1.png
doc/mix_files/figure-markdown_github/unnamed-chunk-4-1.png
doc/mix_files/figure-markdown_github/unnamed-chunk-7-1.png
doc/mix_files/figure-markdown_github/unnamed-chunk-9-1.png
doc/proj.Rmd
doc/proj.md
doc/proj_files/figure-markdown_github/unnamed-chunk-10-1(1).png
doc/proj_files/figure-markdown_github/unnamed-chunk-10-1.png
doc/proj_files/figure-markdown_github/unnamed-chunk-13-1(1).png
doc/proj_files/figure-markdown_github/unnamed-chunk-13-1.png
doc/proj_files/figure-markdown_github/unnamed-chunk-2-1(1).png
doc/proj_files/figure-markdown_github/unnamed-chunk-2-1.png
doc/proj_files/figure-markdown_github/unnamed-chunk-7-1(1).png
doc/proj_files/figure-markdown_github/unnamed-chunk-7-1.png
doc/step.Rmd
doc/step.md
doc/step_files/figure-markdown_github/unnamed-chunk-2-1.png
doc/step_files/figure-markdown_github/unnamed-chunk-3-1.png
doc/step_files/figure-markdown_github/unnamed-chunk-3-10.png
doc/step_files/figure-markdown_github/unnamed-chunk-3-2.png
doc/step_files/figure-markdown_github/unnamed-chunk-3-3.png
doc/step_files/figure-markdown_github/unnamed-chunk-3-4.png
doc/step_files/figure-markdown_github/unnamed-chunk-3-5.png
doc/step_files/figure-markdown_github/unnamed-chunk-3-6.png
doc/step_files/figure-markdown_github/unnamed-chunk-3-7.png
doc/step_files/figure-markdown_github/unnamed-chunk-3-8.png
doc/step_files/figure-markdown_github/unnamed-chunk-3-9.png
doc/tree.Rmd
doc/tree.md
doc/tree_files/figure-markdown_github/unnamed-chunk-12-1(1).png
doc/tree_files/figure-markdown_github/unnamed-chunk-12-1.png
doc/tree_files/figure-markdown_github/unnamed-chunk-2-1(1).png
doc/tree_files/figure-markdown_github/unnamed-chunk-2-1.png
doc/tree_files/figure-markdown_github/unnamed-chunk-3-1(1).png
doc/tree_files/figure-markdown_github/unnamed-chunk-3-1.png
doc/tree_files/figure-markdown_github/unnamed-chunk-4-1(1).png
doc/tree_files/figure-markdown_github/unnamed-chunk-4-1.png
doc/tree_files/figure-markdown_github/unnamed-chunk-5-1(1).png
doc/tree_files/figure-markdown_github/unnamed-chunk-5-1.png
doc/tree_files/figure-markdown_github/unnamed-chunk-7-1(1).png
doc/tree_files/figure-markdown_github/unnamed-chunk-7-1.png
doc/tree_files/figure-markdown_github/unnamed-chunk-8-1(1).png
doc/tree_files/figure-markdown_github/unnamed-chunk-8-1.png
examples/Buettner.R
examples/BuettnerV2.R
examples/CompareOtherTools.R
examples/Differentiation.R
examples/FinalCombination.R
examples/MostRecent.R
examples/PutAllTogether.R
examples/TestConvergence2.R
examples/Trapnel.R
images/.DS_Store
images/circle/AccCompCirc.png
images/circle/AccCompCirc1.png
images/circle/MSDCirc.png
images/circle/PieChr.png
images/circle/Plot2D.png
images/circle/Plot2D_10.png
images/circle/Plot2D_20.png
images/circle/Plot3D.png
inst/java/VDAOEngine.jar
inst/java/colt.jar
man/ApplytoData.Rd
man/CategoriesOnPath.Rd
man/CheckAndGetPath.Rd
man/CheckDirectionality.Rd
man/CircCor.Rd
man/CircShift.Rd
man/CircleConfiguration.Rd
man/ConstructGraph.Rd
man/ConvertNames.Rd
man/CountPubmedResults.Rd
man/CurveConfiguration.Rd
man/DefaultPrincipalTreeConfiguration.Rd
man/DistanceStatistics.Rd
man/ExtendImplicitStaging.Rd
man/GeneExpressiononPath.Rd
man/GetDirectionalityIndex.Rd
man/GetLongestPath.Rd
man/LoadMatrixMarket.Rd
man/OrderOnPath.Rd
man/PCAOutLiers.Rd
man/PlotOnPath.Rd
man/ProjectOnCircle.Rd
man/ProjectOnPrincipalGraph.Rd
man/Rand.POrd.Cor.Rd
man/RobustPrincipalTreeConfiguration.Rd
man/SelectComputePCA.Rd
man/SelectVM.Rd
man/TwoStagesRobustPrincipalTreeConfiguration.Rd
man/accuracyComplexityPlot.Rd
man/computeElPT.Rd
man/computeElasticPrincipalGraph.Rd
man/getTaxonMap.Rd
man/hello.Rd
man/makeGraph.Rd
man/plotData2D.Rd
man/plotData3D.Rd
man/plotMSDEnergyPlot.Rd
man/plotPieNet.Rd
man/projectPoints.Rd
rpgraph.Rproj
vignettes/Intro.Rmd
vignettes/Simple_Examples.Rmd
