Files in BRL-BCM/MolEndoMatch
Molecular Phenotype Patient Matchmaking
.DS_Store
DESCRIPTION
LICENSE
MolPhenoMatch.Rproj
MolPhenoMatch.pdf
NAMESPACE
R/R_shiny_app/metDataPortal_appFns.r
R/R_shiny_app/metDataPortal_shiny_v1.0.R
R/data.HMDBtoKEGG.r
R/data.LabeltoKEGG.R
R/data.fitDataToNormal.r
R/data.getMSEA.r
R/data.getMSEA_Metabolon.r
R/data.quantileNormalize.r
R/plot.getPathviewImage.r
R/plot.pathwayMap.r
README.md
data/.DS_Store
data/Miller2015_Heparin.txt
data/Wangler2017_EDTA.txt
data/heparin_metabolites.txt
data/testData.txt
inst/.DS_Store
inst/extdata/.DS_Store
inst/extdata/Arginine-Metabolism/Arginine-Metabolism.gml
inst/extdata/Arginine-Metabolism/CompoundType-Arginine-Metabolism.txt
inst/extdata/Arginine-Metabolism/DisplayName-Arginine-Metabolism.txt
inst/extdata/Ascorbate-Metabolism/Ascorbate-Metabolism.gml
inst/extdata/Ascorbate-Metabolism/CompoundType-Ascorbate-Metabolism.txt
inst/extdata/Ascorbate-Metabolism/DisplayName-Ascorbate-Metabolism.txt
inst/extdata/Asp-Glu-Metabolism/Asp-Glu-Metabolism.gml
inst/extdata/Asp-Glu-Metabolism/CompoundType-Asp-Glu-Metabolism.txt
inst/extdata/Asp-Glu-Metabolism/DisplayName-Asp-Glu-Metabolism.txt
inst/extdata/BCAA-Metabolism/BCAA-Metabolism.gml
inst/extdata/BCAA-Metabolism/CompoundType-BCAA-Metabolism.txt
inst/extdata/BCAA-Metabolism/DisplayName-BCAA-Metabolism.txt
inst/extdata/Benzoate-Metabolism/Benzoate-Metabolism.gml
inst/extdata/Benzoate-Metabolism/CompoundType-Benzoate-Metabolism.txt
inst/extdata/Benzoate-Metabolism/DisplayName-Benzoate-Metabolism.txt
inst/extdata/Beta-Oxidation/Beta-Oxidation.gml
inst/extdata/Beta-Oxidation/CompoundType-Beta-Oxidation.txt
inst/extdata/Beta-Oxidation/DisplayName-Beta-Oxidation.txt
inst/extdata/Bile-Acid-Metabolism/Bile-Acid-Metabolism.gml
inst/extdata/Bile-Acid-Metabolism/CompoundType-Bile-Acid-Metabolism.txt
inst/extdata/Bile-Acid-Metabolism/DisplayName-Bile-Acid-Metabolism.txt
inst/extdata/Carbamoylphosphate-Pathway/Carbamoylphosphate-Pathway.gml
inst/extdata/Carbamoylphosphate-Pathway/CompoundType-Carbamoylphosphate-Pathway.txt
inst/extdata/Carbamoylphosphate-Pathway/DisplayName-Carbamoylphosphate-Pathway.txt
inst/extdata/Carnitine-Biosynthesis/Carnitine-Biosynthesis.gml
inst/extdata/Carnitine-Biosynthesis/CompoundType-Carnitine-Biosynthesis.txt
inst/extdata/Carnitine-Biosynthesis/DisplayName-Carnitine-Biosynthesis.txt
inst/extdata/Cholesterol-Synthesis/Cholesterol-Synthesis.gml
inst/extdata/Cholesterol-Synthesis/CompoundType-Cholesterol-Synthesis.txt
inst/extdata/Cholesterol-Synthesis/DisplayName-Cholesterol-Synthesis.txt
inst/extdata/Creatine-Metabolism/CompoundType-Creatine-Metabolism.txt
inst/extdata/Creatine-Metabolism/Creatine-Metabolism.gml
inst/extdata/Creatine-Metabolism/DisplayName-Creatine-Metabolism.txt
inst/extdata/DicarboxylicAcid-Metabolism/CompoundType-DicarboxylicAcid-Metabolism.txt
inst/extdata/DicarboxylicAcid-Metabolism/DicarboxylicAcid-Metabolism.gml
inst/extdata/DicarboxylicAcid-Metabolism/DisplayName-DicarboxylicAcid-Metabolism.txt
inst/extdata/Eicosanoids/CompoundType-Eicosanoids.txt
inst/extdata/Eicosanoids/DisplayName-Eicosanoids.txt
inst/extdata/Eicosanoids/Eicosanoids.gml
inst/extdata/Endocannabinoid-Synthesis/CompoundType-Endocannabinoid-Synthesis.txt
inst/extdata/Endocannabinoid-Synthesis/DisplayName-Endocannabinoid-Synthesis.txt
inst/extdata/Endocannabinoid-Synthesis/Endocannabinoid-Synthesis.gml
inst/extdata/FattyAcid-Metabolism/CompoundType-FattyAcid-Metabolism.txt
inst/extdata/FattyAcid-Metabolism/DisplayName-FattyAcid-Metabolism.txt
inst/extdata/FattyAcid-Metabolism/FattyAcid-Metabolism.gml
inst/extdata/Fibrinogen-Cleavage-Peptides/CompoundType-Fibrinogen-Cleavage-Peptides.txt
inst/extdata/Fibrinogen-Cleavage-Peptides/DisplayName-Fibrinogen-Cleavage-Peptides.txt
inst/extdata/Fibrinogen-Cleavage-Peptides/Fibrinogen-Cleavage-Peptides.gml
inst/extdata/GABA-Shunt/CompoundType-GABA-Shunt.txt
inst/extdata/GABA-Shunt/DisplayName-GABA-Shunt.txt
inst/extdata/GABA-Shunt/GABA-Shunt.gml
inst/extdata/Galactose-Metabolism/CompoundType-Galactose-Metabolism.txt
inst/extdata/Galactose-Metabolism/DisplayName-Galactose-Metabolism.txt
inst/extdata/Galactose-Metabolism/Galactose-Metabolism.gml
inst/extdata/Glutathione-Metabolism/CompoundType-Glutathione-Metabolism.txt
inst/extdata/Glutathione-Metabolism/DisplayName-Glutathione-Metabolism.txt
inst/extdata/Glutathione-Metabolism/Glutathione-Metabolism.gml
inst/extdata/Gly-Ser-Thr-Metabolism/CompoundType-Gly-Ser-Thr-Metabolism.txt
inst/extdata/Gly-Ser-Thr-Metabolism/DisplayName-Gly-Ser-Thr-Metabolism.txt
inst/extdata/Gly-Ser-Thr-Metabolism/Gly-Ser-Thr-Metabolism.gml
inst/extdata/Glycogen-Metabolism/.DS_Store
inst/extdata/Glycogen-Metabolism/CompoundType-Glycogen-Metabolism.txt
inst/extdata/Glycogen-Metabolism/DisplayName-Glycogen-Metabolism.txt
inst/extdata/Glycogen-Metabolism/Glycogen-Metabolism.gml
inst/extdata/Glycolysis/CompoundType-Glycolysis.txt
inst/extdata/Glycolysis/DisplayName-Glycolysis.txt
inst/extdata/Glycolysis/Glycolysis.gml
inst/extdata/Glycosylation/CompoundType-Glycosylation.txt
inst/extdata/Glycosylation/DisplayName-Glycosylation.txt
inst/extdata/Glycosylation/Glycosylation.gml
inst/extdata/Hemoglobin-Porphyrin-Metabolism/CompoundType-Hemoglobin-Porphyrin-Metabolism.txt
inst/extdata/Hemoglobin-Porphyrin-Metabolism/DisplayName-Hemoglobin-Porphyrin-Metabolism.txt
inst/extdata/Hemoglobin-Porphyrin-Metabolism/Hemoglobin-Porphyrin-Metabolism.gml
inst/extdata/Histidine-Metabolism/CompoundType-Histidine-Metabolism.txt
inst/extdata/Histidine-Metabolism/DisplayName-Histidine-Metabolism.txt
inst/extdata/Histidine-Metabolism/Histidine-Metabolism.gml
inst/extdata/Inositol-Metabolism/CompoundType-Inositol-Metabolism.txt
inst/extdata/Inositol-Metabolism/DisplayName-Inositol-Metabolism.txt
inst/extdata/Inositol-Metabolism/Inositol-Metabolism.gml
inst/extdata/Ketone-Bodies/CompoundType-Ketone-Bodies.txt
inst/extdata/Ketone-Bodies/DisplayName-Ketone-Bodies.txt
inst/extdata/Ketone-Bodies/Ketone-Bodies.gml
inst/extdata/Lysine-Catabolism/CompoundType-Lysine-Catabolism.txt
inst/extdata/Lysine-Catabolism/DisplayName-Lysine-Catabolism.txt
inst/extdata/Lysine-Catabolism/Lysine-Catabolism.gml
inst/extdata/Met-Cys-Metabolism/CompoundType-Met-Cys-Metabolism.txt
inst/extdata/Met-Cys-Metabolism/DisplayName-Met-Cys-Metabolism.txt
inst/extdata/Met-Cys-Metabolism/Met-Cys-Metabolism.gml
inst/extdata/Mevalonate-Metabolism/CompoundType-Mevalonate-Metabolism.txt
inst/extdata/Mevalonate-Metabolism/DisplayName-Mevalonate-Metabolism.txt
inst/extdata/Mevalonate-Metabolism/Mevalonate-Metabolism.gml
inst/extdata/Nicotinate-Nicotinamide-Metabolism/CompoundType-Nicotinate-Nicotinamide-Metabolism.txt
inst/extdata/Nicotinate-Nicotinamide-Metabolism/DisplayName-Nicotinate-Nicotinamide-Metabolism.txt
inst/extdata/Nicotinate-Nicotinamide-Metabolism/Nicotinate-Nicotinamide-Metabolism.gml
inst/extdata/Pantothenate-Metabolism/CompoundType-Pantothenate-Metabolism.txt
inst/extdata/Pantothenate-Metabolism/DisplayName-Pantothenate-Metabolism.txt
inst/extdata/Pantothenate-Metabolism/Pantothenate-Metabolism.gml
inst/extdata/Pentose-Phosphate-Metabolism/CompoundType-Pentose-Phosphate-Metabolism.txt
inst/extdata/Pentose-Phosphate-Metabolism/DisplayName-Pentose-Phosphate-Metabolism.txt
inst/extdata/Pentose-Phosphate-Metabolism/Pentose-Phosphate-Metabolism.gml
inst/extdata/Phe-Tyr-Metabolism/CompoundType-Phe-Tyr-Metabolism.txt
inst/extdata/Phe-Tyr-Metabolism/DisplayName-Phe-Tyr-Metabolism.txt
inst/extdata/Phe-Tyr-Metabolism/Phe-Tyr-Metabolism.gml
inst/extdata/Phospholipid-Metabolism/CompoundType-Phospholipid-Metabolism.txt
inst/extdata/Phospholipid-Metabolism/DisplayName-Phospholipid-Metabolism.txt
inst/extdata/Phospholipid-Metabolism/Phospholipid-Metabolism.gml
inst/extdata/Polyamine-Metabolism/CompoundType-Polyamine-Metabolism.txt
inst/extdata/Polyamine-Metabolism/DisplayName-Polyamine-Metabolism.txt
inst/extdata/Polyamine-Metabolism/Polyamine-Metabolism.gml
inst/extdata/Proline-Metabolism/CompoundType-Proline-Metabolism.txt
inst/extdata/Proline-Metabolism/DisplayName-Proline-Metabolism.txt
inst/extdata/Proline-Metabolism/Proline-Metabolism.gml
inst/extdata/Protein-Degradation/CompoundType-Protein-Degradation.txt
inst/extdata/Protein-Degradation/DisplayName-Protein-Degradation.txt
inst/extdata/Protein-Degradation/Protein-Degradation.gml
inst/extdata/Purine-Metabolism/CompoundType-Purine-Metabolism.txt
inst/extdata/Purine-Metabolism/DisplayName-Purine-Metabolism.txt
inst/extdata/Purine-Metabolism/Purine-Metabolism.gml
inst/extdata/Pyridoxal-Metabolism/CompoundType-Pyridoxal-Metabolism.txt
inst/extdata/Pyridoxal-Metabolism/DisplayName-Pyridoxal-Metabolism.txt
inst/extdata/Pyridoxal-Metabolism/Pyridoxal-Metabolism.gml
inst/extdata/Pyrimidine-Metabolism/.DS_Store
inst/extdata/Pyrimidine-Metabolism/CompoundType-Pyrimidine-Metabolism.txt
inst/extdata/Pyrimidine-Metabolism/DisplayName-Pyrimidine-Metabolism.txt
inst/extdata/Pyrimidine-Metabolism/Pyrimidine-Metabolism.gml
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/RData/allPathways2.RData
inst/extdata/Riboflavin-Metabolism/CompoundType-Riboflavin-Metabolism.txt
inst/extdata/Riboflavin-Metabolism/DisplayName-Riboflavin-Metabolism.txt
inst/extdata/Riboflavin-Metabolism/Riboflavin-Metabolism.gml
inst/extdata/Secondary-Bile-Acids/CompoundType-Secondary-Bile-Acids.txt
inst/extdata/Secondary-Bile-Acids/DisplayName-Secondary-Bile-Acids.txt
inst/extdata/Secondary-Bile-Acids/Secondary-Bile-Acids.gml
inst/extdata/Sorbitol-Glycerol-Metabolism/CompoundType-Sorbitol-Glycerol-Metabolism.txt
inst/extdata/Sorbitol-Glycerol-Metabolism/DisplayName-Sorbitol-Glycerol-Metabolism.txt
inst/extdata/Sorbitol-Glycerol-Metabolism/Sorbitol-Glycerol-Metabolism.gml
inst/extdata/Sphingolipid-Metabolism/CompoundType-Sphingolipid-Metabolism.txt
inst/extdata/Sphingolipid-Metabolism/DisplayName-Sphingolipid-Metabolism.txt
inst/extdata/Sphingolipid-Metabolism/Sphingolipid-Metabolism.gml
inst/extdata/Steroid-Hormone-Biosynthesis/CompoundType-Steroid-Hormone-Biosynthesis.txt
inst/extdata/Steroid-Hormone-Biosynthesis/DisplayName-Steroid-Hormone-Biosynthesis.txt
inst/extdata/Steroid-Hormone-Biosynthesis/Steroid-Hormone-Biosynthesis.gml
inst/extdata/TCA-Cycle/CompoundType-TCA-Cycle.txt
inst/extdata/TCA-Cycle/DisplayName-TCA-Cycle.txt
inst/extdata/TCA-Cycle/TCA-Cycle.gml
inst/extdata/Thyroid-Hormone-Synthesis/CompoundType-Thyroid-Hormone-Synthesis.txt
inst/extdata/Thyroid-Hormone-Synthesis/DisplayName-Thyroid-Hormone-Synthesis.txt
inst/extdata/Thyroid-Hormone-Synthesis/Thyroid-Hormone-Synthesis.gml
inst/extdata/Tryptophan-Metabolism/CompoundType-Tryptophan-Metabolism.txt
inst/extdata/Tryptophan-Metabolism/DisplayName-Tryptophan-Metabolism.txt
inst/extdata/Tryptophan-Metabolism/Tryptophan-Metabolism.gml
inst/extdata/allPathways/CompoundType-allPathways.txt
inst/extdata/allPathways/DisplayName-allPathways.txt
inst/extdata/allPathways/allPathways.gml
inst/extdata/complexNodes.RData
inst/extdata/metabolon_to_data.txt
main_molphenomatch.r
man/data.HMDBtoKEGG.Rd
man/data.LabeltoKEGG.Rd
man/data.fitDataToNormal.Rd
man/data.getMSEA.Rd
man/data.getMSEA_Metabolon.Rd
man/data.quantileNormalize.Rd
man/plot.getPathviewImage.Rd
man/plot.pathwayMap.Rd
