Files in BRL-BCM/CTD
CTD method for “connecting the dots” in weighted graphs

.gitignore
CTD.Rproj
CTD.pdf
DESCRIPTION
LICENSE
NAMESPACE
R/data.HMDBtoKEGG.r R/data.LabeltoKEGG.r R/data.Miller2015.r R/data.Wangler2017.r R/data.surrogateProfiles.r R/graph.diffuseP1.r R/graph.diffuseP1Movie.r R/graph.naivePruning.r R/mle.blowoutPtSim.r R/mle.getEncodingLength.r R/mle.getMinPtDistance.r R/mle.getPtSim.r R/mle.kraftMcMillan.r R/multiNode.getNodeRanks.r R/multiNode.getNodeRanksMovie.r R/multiNode.getPtBSbyK.r R/pathway.ListMaps_metabolon.r R/pathway.ListMetabolites_metabolon.r R/plot.getPathwayIgraph.r R/plot.hmSim.r R/plot.knnSim.r R/plot.mdsSim.r R/plot.pathwayMap.r R/singleNode.getNodeRanksMovie.r R/singleNode.getNodeRanksN.r R/singleNode.getPtBSbyK.r R/stats.entropyFunction.r R/stats.fishersMethod.r R/stats.getMSEA_Metabolon.r R/stats.getORA_Metabolon.r README.md
data/Miller2015.RData
data/Thistlethwaite2019.RData
data/Wangler2017.RData
inst/extdata/Arginine-Metabolism/Arginine-Metabolism.gml
inst/extdata/Arginine-Metabolism/Name-Arginine-Metabolism.txt
inst/extdata/Arginine-Metabolism/Type-Arginine-Metabolism.txt
inst/extdata/Ascorbate-Metabolism/Ascorbate-Metabolism.gml
inst/extdata/Ascorbate-Metabolism/Name-Ascorbate-Metabolism.txt
inst/extdata/Ascorbate-Metabolism/Type-Ascorbate-Metabolism.txt
inst/extdata/Asp-Glu-Metabolism/Asp-Glu-Metabolism.gml
inst/extdata/Asp-Glu-Metabolism/Name-Asp-Glu-Metabolism.txt
inst/extdata/Asp-Glu-Metabolism/Type-Asp-Glu-Metabolism.txt
inst/extdata/BCAA-Metabolism/BCAA-Metabolism.gml
inst/extdata/BCAA-Metabolism/Name-BCAA-Metabolism.txt
inst/extdata/BCAA-Metabolism/Type-BCAA-Metabolism.txt
inst/extdata/Benzoate-Metabolism/Benzoate-Metabolism.gml
inst/extdata/Benzoate-Metabolism/Name-Benzoate-Metabolism.txt
inst/extdata/Benzoate-Metabolism/Type-Benzoate-Metabolism.txt
inst/extdata/Beta-Oxidation/Beta-Oxidation.gml
inst/extdata/Beta-Oxidation/Name-Beta-Oxidation.txt
inst/extdata/Beta-Oxidation/Type-Beta-Oxidation.txt
inst/extdata/Bile-Acid-Metabolism/Bile-Acid-Metabolism.gml
inst/extdata/Bile-Acid-Metabolism/Name-Bile-Acid-Metabolism.txt
inst/extdata/Bile-Acid-Metabolism/Type-Bile-Acid-Metabolism.txt
inst/extdata/Carbamoylphosphate-Pathway/Carbamoylphosphate-Pathway.gml
inst/extdata/Carbamoylphosphate-Pathway/Name-Carbamoylphosphate-Pathway.txt
inst/extdata/Carbamoylphosphate-Pathway/Type-Carbamoylphosphate-Pathway.txt
inst/extdata/Carnitine-Biosynthesis/Carnitine-Biosynthesis.gml
inst/extdata/Carnitine-Biosynthesis/Name-Carnitine-Biosynthesis.txt
inst/extdata/Carnitine-Biosynthesis/Type-Carnitine-Biosynthesis.txt
inst/extdata/Cholesterol-Synthesis/Cholesterol-Synthesis.gml
inst/extdata/Cholesterol-Synthesis/Name-Cholesterol-Synthesis.txt
inst/extdata/Cholesterol-Synthesis/Type-Cholesterol-Synthesis.txt
inst/extdata/Creatine-Metabolism/Creatine-Metabolism.gml
inst/extdata/Creatine-Metabolism/Name-Creatine-Metabolism.txt
inst/extdata/Creatine-Metabolism/Type-Creatine-Metabolism.txt
inst/extdata/DicarboxylicAcid-Metabolism/DicarboxylicAcid-Metabolism.gml
inst/extdata/DicarboxylicAcid-Metabolism/Name-DicarboxylicAcid-Metabolism.txt
inst/extdata/DicarboxylicAcid-Metabolism/Type-DicarboxylicAcid-Metabolism.txt
inst/extdata/Eicosanoids/Eicosanoids.gml
inst/extdata/Eicosanoids/Name-Eicosanoids.txt
inst/extdata/Eicosanoids/Type-Eicosanoids.txt
inst/extdata/Endocannabinoid-Synthesis/Endocannabinoid-Synthesis.gml
inst/extdata/Endocannabinoid-Synthesis/Name-Endocannabinoid-Synthesis.txt
inst/extdata/Endocannabinoid-Synthesis/Type-Endocannabinoid-Synthesis.txt
inst/extdata/FattyAcid-Metabolism/FattyAcid-Metabolism.gml
inst/extdata/FattyAcid-Metabolism/Name-FattyAcid-Metabolism.txt
inst/extdata/FattyAcid-Metabolism/Type-FattyAcid-Metabolism.txt
inst/extdata/Fibrinogen-Cleavage-Peptides/Fibrinogen-Cleavage-Peptides.gml
inst/extdata/Fibrinogen-Cleavage-Peptides/Name-Fibrinogen-Cleavage-Peptides.txt
inst/extdata/Fibrinogen-Cleavage-Peptides/Type-Fibrinogen-Cleavage-Peptides.txt
inst/extdata/GABA-Shunt/GABA-Shunt.gml
inst/extdata/GABA-Shunt/Name-GABA-Shunt.txt
inst/extdata/GABA-Shunt/Type-GABA-Shunt.txt
inst/extdata/Galactose-Metabolism/Galactose-Metabolism.gml
inst/extdata/Galactose-Metabolism/Name-Galactose-Metabolism.txt
inst/extdata/Galactose-Metabolism/Type-Galactose-Metabolism.txt
inst/extdata/Glutathione-Metabolism/Glutathione-Metabolism.gml
inst/extdata/Glutathione-Metabolism/Name-Glutathione-Metabolism.txt
inst/extdata/Glutathione-Metabolism/Type-Glutathione-Metabolism.txt
inst/extdata/Gly-Ser-Thr-Metabolism/Gly-Ser-Thr-Metabolism.gml
inst/extdata/Gly-Ser-Thr-Metabolism/Name-Gly-Ser-Thr-Metabolism.txt
inst/extdata/Gly-Ser-Thr-Metabolism/Type-Gly-Ser-Thr-Metabolism.txt
inst/extdata/Glycogen-Metabolism/Glycogen-Metabolism.gml
inst/extdata/Glycogen-Metabolism/Name-Glycogen-Metabolism.txt
inst/extdata/Glycogen-Metabolism/Type-Glycogen-Metabolism.txt
inst/extdata/Glycolysis/Glycolysis.gml
inst/extdata/Glycolysis/Name-Glycolysis.txt
inst/extdata/Glycolysis/Type-Glycolysis.txt
inst/extdata/Glycosylation/Glycosylation.gml
inst/extdata/Glycosylation/Name-Glycosylation.txt
inst/extdata/Glycosylation/Type-Glycosylation.txt
inst/extdata/Hemoglobin-Porphyrin-Metabolism/Hemoglobin-Porphyrin-Metabolism.gml
inst/extdata/Hemoglobin-Porphyrin-Metabolism/Name-Hemoglobin-Porphyrin-Metabolism.txt
inst/extdata/Hemoglobin-Porphyrin-Metabolism/Type-Hemoglobin-Porphyrin-Metabolism.txt
inst/extdata/Histidine-Metabolism/Histidine-Metabolism.gml
inst/extdata/Histidine-Metabolism/Name-Histidine-Metabolism.txt
inst/extdata/Histidine-Metabolism/Type-Histidine-Metabolism.txt
inst/extdata/Inositol-Metabolism/Inositol-Metabolism.gml
inst/extdata/Inositol-Metabolism/Name-Inositol-Metabolism.txt
inst/extdata/Inositol-Metabolism/Type-Inositol-Metabolism.txt
inst/extdata/Ketone-Bodies/Ketone-Bodies.gml
inst/extdata/Ketone-Bodies/Name-Ketone-Bodies.txt
inst/extdata/Ketone-Bodies/Type-Ketone-Bodies.txt
inst/extdata/Lysine-Catabolism/Lysine-Catabolism.gml
inst/extdata/Lysine-Catabolism/Name-Lysine-Catabolism.txt
inst/extdata/Lysine-Catabolism/Type-Lysine-Catabolism.txt
inst/extdata/MSEA_Datasets/Burrage2019.gct
inst/extdata/MSEA_Datasets/Burrage2019_arg.cls
inst/extdata/MSEA_Datasets/Burrage2019_asld.cls
inst/extdata/MSEA_Datasets/Burrage2019_otc.cls
inst/extdata/MSEA_Datasets/EDTA_aadc.cls
inst/extdata/MSEA_Datasets/EDTA_aadc.gct
inst/extdata/MSEA_Datasets/EDTA_abat.cls
inst/extdata/MSEA_Datasets/EDTA_abat.gct
inst/extdata/MSEA_Datasets/EDTA_adsl.cls
inst/extdata/MSEA_Datasets/EDTA_adsl.gct
inst/extdata/MSEA_Datasets/Miller2015.gct
inst/extdata/MSEA_Datasets/Miller2015_arg.cls
inst/extdata/MSEA_Datasets/Wangler2017.gct
inst/extdata/MSEA_Datasets/Wangler2017_pex1.cls
inst/extdata/MSEA_Datasets/Wangler2017_pex6.cls
inst/extdata/MSEA_Datasets/Wangler2017_pex7.cls
inst/extdata/Met-Cys-Metabolism/Met-Cys-Metabolism.gml
inst/extdata/Met-Cys-Metabolism/Name-Met-Cys-Metabolism.txt
inst/extdata/Met-Cys-Metabolism/Type-Met-Cys-Metabolism.txt
inst/extdata/Mevalonate-Metabolism/Mevalonate-Metabolism.gml
inst/extdata/Mevalonate-Metabolism/Name-Mevalonate-Metabolism.txt
inst/extdata/Mevalonate-Metabolism/Type-Mevalonate-Metabolism.txt
inst/extdata/Nicotinate-Nicotinamide-Metabolism/Name-Nicotinate-Nicotinamide-Metabolism.txt
inst/extdata/Nicotinate-Nicotinamide-Metabolism/Nicotinate-Nicotinamide-Metabolism.gml
inst/extdata/Nicotinate-Nicotinamide-Metabolism/Type-Nicotinate-Nicotinamide-Metabolism.txt
inst/extdata/Pantothenate-Metabolism/Name-Pantothenate-Metabolism.txt
inst/extdata/Pantothenate-Metabolism/Pantothenate-Metabolism.gml
inst/extdata/Pantothenate-Metabolism/Type-Pantothenate-Metabolism.txt
inst/extdata/Pathway_GMTs/Metabolon.gmt
inst/extdata/Pentose-Phosphate-Metabolism/Name-Pentose-Phosphate-Metabolism.txt
inst/extdata/Pentose-Phosphate-Metabolism/Pentose-Phosphate-Metabolism.gml
inst/extdata/Pentose-Phosphate-Metabolism/Type-Pentose-Phosphate-Metabolism.txt
inst/extdata/Phe-Tyr-Metabolism/Name-Phe-Tyr-Metabolism.txt
inst/extdata/Phe-Tyr-Metabolism/Phe-Tyr-Metabolism.gml
inst/extdata/Phe-Tyr-Metabolism/Type-Phe-Tyr-Metabolism.txt
inst/extdata/Phospholipid-Metabolism/Name-Phospholipid-Metabolism.txt
inst/extdata/Phospholipid-Metabolism/Phospholipid-Metabolism.gml
inst/extdata/Phospholipid-Metabolism/Type-Phospholipid-Metabolism.txt
inst/extdata/Polyamine-Metabolism/Name-Polyamine-Metabolism.txt
inst/extdata/Polyamine-Metabolism/Polyamine-Metabolism.gml
inst/extdata/Polyamine-Metabolism/Type-Polyamine-Metabolism.txt
inst/extdata/Proline-Metabolism/Name-Proline-Metabolism.txt
inst/extdata/Proline-Metabolism/Proline-Metabolism.gml
inst/extdata/Proline-Metabolism/Type-Proline-Metabolism.txt
inst/extdata/Protein-Degradation/Name-Protein-Degradation.txt
inst/extdata/Protein-Degradation/Protein-Degradation.gml
inst/extdata/Protein-Degradation/Type-Protein-Degradation.txt
inst/extdata/Purine-Metabolism/Name-Purine-Metabolism.txt
inst/extdata/Purine-Metabolism/Purine-Metabolism.gml
inst/extdata/Purine-Metabolism/Type-Purine-Metabolism.txt
inst/extdata/Pyridoxal-Metabolism/Name-Pyridoxal-Metabolism.txt
inst/extdata/Pyridoxal-Metabolism/Pyridoxal-Metabolism.gml
inst/extdata/Pyridoxal-Metabolism/Type-Pyridoxal-Metabolism.txt
inst/extdata/Pyrimidine-Metabolism/Name-Pyrimidine-Metabolism.txt
inst/extdata/Pyrimidine-Metabolism/Pyrimidine-Metabolism.gml
inst/extdata/Pyrimidine-Metabolism/Type-Pyrimidine-Metabolism.txt
inst/extdata/RData/Arginine-Metabolism.RData
inst/extdata/RData/Ascorbate-Metabolism.RData
inst/extdata/RData/Asp-Glu-Metabolism.RData
inst/extdata/RData/BCAA-Metabolism.RData
inst/extdata/RData/Benzoate-Metabolism.RData
inst/extdata/RData/Beta-Oxidation.RData
inst/extdata/RData/Bile-Acid-Metabolism.RData
inst/extdata/RData/Carbamoylphosphate-Pathway.RData
inst/extdata/RData/Carnitine-Biosynthesis.RData
inst/extdata/RData/Cholesterol-Synthesis.RData
inst/extdata/RData/Creatine-Metabolism.RData
inst/extdata/RData/DicarboxylicAcid-Metabolism.RData
inst/extdata/RData/Eicosanoids.RData
inst/extdata/RData/Endocannabinoid-Synthesis.RData
inst/extdata/RData/FattyAcid-Metabolism.RData
inst/extdata/RData/Fibrinogen-Cleavage-Peptides.RData
inst/extdata/RData/GABA-Shunt.RData
inst/extdata/RData/Galactose-Metabolism.RData
inst/extdata/RData/Glutathione-Metabolism.RData
inst/extdata/RData/Gly-Ser-Thr-Metabolism.RData
inst/extdata/RData/Glycogen-Metabolism.RData
inst/extdata/RData/Glycolysis.RData
inst/extdata/RData/Glycosylation.RData
inst/extdata/RData/Hemoglobin-Porphyrin-Metabolism.RData
inst/extdata/RData/Histidine-Metabolism.RData
inst/extdata/RData/Inositol-Metabolism.RData
inst/extdata/RData/Ketone-Bodies.RData
inst/extdata/RData/Lysine-Catabolism.RData
inst/extdata/RData/Met-Cys-Metabolism.RData
inst/extdata/RData/Mevalonate-Metabolism.RData
inst/extdata/RData/Nicotinate-Nicotinamide-Metabolism.RData
inst/extdata/RData/Pantothenate-Metabolism.RData
inst/extdata/RData/Pentose-Phosphate-Metabolism.RData
inst/extdata/RData/Phe-Tyr-Metabolism.RData
inst/extdata/RData/Phospholipid-Metabolism.RData
inst/extdata/RData/Polyamine-Metabolism.RData
inst/extdata/RData/Proline-Metabolism.RData
inst/extdata/RData/Protein-Degradation.RData
inst/extdata/RData/Purine-Metabolism.RData
inst/extdata/RData/Pyridoxal-Metabolism.RData
inst/extdata/RData/Pyrimidine-Metabolism.RData
inst/extdata/RData/Riboflavin-Metabolism.RData
inst/extdata/RData/Secondary-Bile-Acids.RData
inst/extdata/RData/Sorbitol-Glycerol-Metabolism.RData
inst/extdata/RData/Sphingolipid-Metabolism.RData
inst/extdata/RData/Steroid-Hormone-Biosynthesis.RData
inst/extdata/RData/TCA-Cycle.RData
inst/extdata/RData/Thyroid-Hormone-Synthesis.RData
inst/extdata/RData/Tryptophan-Metabolism.RData
inst/extdata/RData/allPathways.RData
inst/extdata/Riboflavin-Metabolism/Name-Riboflavin-Metabolism.txt
inst/extdata/Riboflavin-Metabolism/Riboflavin-Metabolism.gml
inst/extdata/Riboflavin-Metabolism/Type-Riboflavin-Metabolism.txt
inst/extdata/Secondary-Bile-Acids/Name-Secondary-Bile-Acids.txt
inst/extdata/Secondary-Bile-Acids/Secondary-Bile-Acids.gml
inst/extdata/Secondary-Bile-Acids/Type-Secondary-Bile-Acids.txt
inst/extdata/Sorbitol-Glycerol-Metabolism/Name-Sorbitol-Glycerol-Metabolism.txt
inst/extdata/Sorbitol-Glycerol-Metabolism/Sorbitol-Glycerol-Metabolism.gml
inst/extdata/Sorbitol-Glycerol-Metabolism/Type-Sorbitol-Glycerol-Metabolism.txt
inst/extdata/Sphingolipid-Metabolism/Name-Sphingolipid-Metabolism.txt
inst/extdata/Sphingolipid-Metabolism/Sphingolipid-Metabolism.gml
inst/extdata/Sphingolipid-Metabolism/Type-Sphingolipid-Metabolism.txt
inst/extdata/Steroid-Hormone-Biosynthesis/Name-Steroid-Hormone-Biosynthesis.txt
inst/extdata/Steroid-Hormone-Biosynthesis/Steroid-Hormone-Biosynthesis.gml
inst/extdata/Steroid-Hormone-Biosynthesis/Type-Steroid-Hormone-Biosynthesis.txt
inst/extdata/TCA-Cycle/Name-TCA-Cycle.txt
inst/extdata/TCA-Cycle/TCA-Cycle.gml
inst/extdata/TCA-Cycle/Type-TCA-Cycle.txt
inst/extdata/Thyroid-Hormone-Synthesis/Name-Thyroid-Hormone-Synthesis.txt
inst/extdata/Thyroid-Hormone-Synthesis/Thyroid-Hormone-Synthesis.gml
inst/extdata/Thyroid-Hormone-Synthesis/Type-Thyroid-Hormone-Synthesis.txt
inst/extdata/Tryptophan-Metabolism/Name-Tryptophan-Metabolism.txt
inst/extdata/Tryptophan-Metabolism/Tryptophan-Metabolism.gml
inst/extdata/Tryptophan-Metabolism/Type-Tryptophan-Metabolism.txt
inst/extdata/allPathways/Name-allPathways.txt
inst/extdata/allPathways/Type-allPathways.txt
inst/extdata/allPathways/allPathways.gml
inst/extdata/complexNodes.RData
inst/extdata/metabolon_to_data.txt
man/data.HMDBtoKEGG.Rd man/data.LabeltoKEGG.Rd man/data.surrogateProfiles.Rd man/graph.diffuseP1.Rd man/graph.diffuseP1Movie.Rd man/graph.naivePruning.Rd man/mle.blowoutSim.Rd man/mle.getEncodingLength.Rd man/mle.getMinPtDistance.Rd man/mle.getPtSim.Rd man/mle.kraftMcMillan.Rd man/multiNode.getNodeRanks.Rd man/multiNode.getNodeRanksMovie.Rd man/multiNode.getPtBSbyK.Rd man/pathway.ListMaps_metabolon.Rd man/pathway.ListMetabolites_metabolon.Rd man/plot.getPathwayIgraph.Rd man/plot.hmSim.Rd man/plot.knnSim.Rd man/plot.mdsSim.Rd man/plot.pathwayMap.Rd man/singleNode.getNodeRanksMovie.Rd man/singleNode.getNodeRanksN.Rd man/singleNode.getPtBSbyK.Rd man/stats.entropyFunction.Rd man/stats.fishersMethod.Rd man/stats.getMSEA_Metabolon.Rd man/stats.getORA_Metabolon.Rd vignette/CTD_Lab-Exercise.Rmd
vignette/CTD_Lab-Exercise.html
vignette/images/probability_diffusion.svg
vignette/r-env-setup-script.R
BRL-BCM/CTD documentation built on Nov. 11, 2019, 10:03 p.m.