├── DESCRIPTION ├── GeneSetClustes.v1.2.Rproj ├── LICENSE ├── NAMESPACE ├── R ├── BreakUpCluster.R ├── ClusterGeneSets.R ├── CombineGeneSets.R ├── GeneSetCluster.R ├── GeneSetCluster.pipeline ├── GenesPerGeneSet.r ├── GenesPerGeneset.Count.fc ├── GetOptimalCluster.R ├── GetSTRINGdbPerGeneSets.R ├── HighlightGeneSets.R ├── LoadGeneSets.R ├── ManageGeneSets.R ├── MeanClusterDifferences.R ├── MergeObjects.R ├── ORAGeneSets.R ├── ObjectCreator.R ├── OptimalGeneSets.R ├── PathwayObject.R ├── PlotGeneDedrogram.R ├── PlotGeneNetworks.R ├── PlotGeneSets.R ├── RR_stats ├── ShowExperimentdata.R ├── ShowGeneSets.R ├── ShowMeta.R ├── Umap.3d_Interactive.GeneSets.R ├── UmapGeneSets.R ├── VennDiagram.R ├── WriteGeneSets.R ├── data.R └── plotSTRINGdbPerGeneSets.R ├── README.md ├── data ├── Redox.genes.rda └── datalist ├── fig ├── BreakUpCluster.V1.png ├── Capture_GenesPerGeneSet_v1.PNG ├── Capture_Loaded_Table_v1.PNG ├── Capture_Loaded_Table_v2.png ├── Capture_Loaded_Table_v3.PNG ├── Capture_STRING_v2.PNG ├── EEWING_Optimal_clustersGAP.png ├── EEWING_Optimal_clusterselbow.png ├── EEWING_Optimal_clusterssilhouette.png ├── Figure1_20190826.png ├── GREAT.load.png ├── GeneSetCluster_Outline_revision.png ├── Highlight_genes.png ├── IPA.LOAD.png ├── Logo.png ├── Logo_small.png ├── Networks_1.png ├── Networks_2.png ├── Networks_3.png ├── Networks_4.png ├── Networks_5.png ├── Object_creator_test.png ├── PathwayObject_content.PNG ├── Venndiagram.png ├── jaccard.png ├── pathways.mtx.png ├── plotgenes.png └── plotgenes2.png ├── inst ├── doc │ ├── GeneSetCluster.R │ ├── GeneSetCluster.html │ └── GeneSetCluster.rmd └── extdata │ ├── MM10.GREAT.KO.uGvsMac.bed.tsv │ ├── MM10.GREAT.KO.uGvsMac.bed_BCKGRND.tsv │ ├── MM10.GREAT.WT.uGvsMac.bed.tsv │ ├── MM10.GREAT.WT.uGvsMac.bed_BCKGRND.tsv │ ├── MM10.IPA.KO.uGvsMac.Canonical_pathways.xls │ ├── MM10.IPA.KO.uGvsMac.Functional_annotations.xls │ ├── MM10.IPA.WT.uGvsMac.Canonical_pathways.xls │ └── MM10.IPA.WT.uGvsMac.Functional_annotations.xls ├── man ├── ClusterGeneSets.Rd ├── CombineGeneSets.Rd ├── GeneSetCluster.Rd ├── GenesPerGeneSet-PathwayObject-method.Rd ├── GenesPerGeneSet.Rd ├── GetSTRINGdbPerGeneSets.Rd ├── HighlightGeneSets.Rd ├── LoadGeneSets.Rd ├── ManageGeneSets.Rd ├── MergeObjects.Rd ├── ORAGeneSets.Rd ├── ObjectCreator.Rd ├── OptimalGeneSets.Rd ├── PathwayObject-class.Rd ├── PlotGeneDendrogram-PathwayObject-method.Rd ├── PlotGeneDendrogram.Rd ├── PlotGeneNetworks-PathwayObject-method.Rd ├── PlotGeneNetworks.Rd ├── PlotGeneSets-PathwayObject-method.Rd ├── PlotGeneSets.Rd ├── Redox.genes.Rd ├── ShowExperimentdata-PathwayObject-method.Rd ├── ShowExperimentdata.Rd ├── ShowGeneSets-PathwayObject-method.Rd ├── ShowGeneSets.Rd ├── ShowMeta-PathwayObject-method.Rd ├── ShowMeta.Rd ├── VennDiagram.Rd ├── WriteGeneSets-PathwayObject-method.Rd ├── WriteGeneSets.Rd └── plotSTRINGdbPerGeneSets.Rd └── vignettes ├── GeneSetCluster.R ├── GeneSetCluster.html ├── GeneSetCluster.rmd 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