Files in asifemon/msdrp
Pathway Signatures 4 Drug Repurposing
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/README.rst
R/analysis/CheckDistribution.R
R/analysis/DiseaseSPIA.R
R/analysis/DrugCombination.R
R/analysis/DrugSPIA.R
R/analysis/README.rst
R/analysis/SignificantOverlap.R
R/analysis/geneVsPathwayCentricComparison.R
R/analysis/ps4dr_ferrero_comparison.R
R/preprocessing/MeSH2EFO.R
R/preprocessing/README.rst
R/preprocessing/RetrieveDEGs.R
R/preprocessing/RetrieveDrugResponseData.R
R/preprocessing/creeds_data_preprocessing.R
README.rst
data/13040_2018_171_MOESM2_ESM.csv
data/13040_2018_171_MOESM3_ESM.csv
data/DEGs.RData
data/EFO.csv
data/GWASs.RData
data/L1000.RData
data/L1000Drugs.csv
data/L1000_raw.RData
data/Predicted-Drugs-with-clinical-Trials-Info.csv
data/README.rst
data/cancerdrugs_NCI.csv
data/cancerdrugs_NCI_28012020.txt
data/chembl_1234.csv
data/creeds/Creeds Loader.ipynb
data/creeds/README.rst
data/creeds/bortezomib_drug_data.tsv
data/creeds/disease_data.json
data/creeds/drug_data.json
data/creeds/gene_data.json
data/creeds/melanoma_disease_data.tsv
data/drug2715details.RData
data/drug2disease.RData
data/geneID_v97.RData
data/img/workflow.jpg
data/lincs_pubchem.RData
data/results/CREEDs/drugCorrelation_result_creeds.RData
data/results/CREEDs/lfc_disease_creeds.RData
data/results/CREEDs/lfc_drug_creeds.RData
data/results/CREEDs/spia_kegg_creeds.RData
data/results/CREEDs/spia_kegg_disease_creeds.RData
data/results/DisPwGeneList.RData
data/results/ROC_result.RDATA
data/results/disease_genes.RData
data/results/drugCombination_CorrelationScore.RData
data/results/drugCombination_result_drugPdisease.RData
data/results/drugCombination_shortlist_breastCancer.csv
data/results/drugCorrelation_result.RData
data/results/drugCorrelation_result_genes_all.RData
data/results/drugCorrelation_result_genes_lfc_2.RData
data/results/drugGWAS_genes.padj1e-10.RData
data/results/drugPdisease_genes.RData
data/results/drugPdisease_genes.padj.RData
data/results/drugPdisease_genes.padj1e-5.RData
data/results/drug_comb_path_drugPdisease.RData
data/results/drug_comparison_ps4dr-ferrero.RData
data/results/drug_comparison_table_ps4dr-ferrero.csv
data/results/drug_shortlist.csv
data/results/drug_shortlist_genes_all.csv
data/results/drug_shortlist_genes_lfc_2.csv
data/results/figures/Figure_1_PS4DR.jpg
data/results/figures/Figure_3_PS4DR.jpg
data/results/figures/Figure_4_PS4DR.jpg
data/results/figures/Geneset_intersection_venn_diagramm.png
data/results/figures/Q-Q_Plots_CorrelationScore_scaled.jpeg
data/results/figures/ScatterPlots_CorrelationScore.html
data/results/figures/ScatterPlots_CorrelationScore.jpeg
data/results/figures/ScatterPlots_combination_Diseases.jpeg
data/results/figures/densityPlots_CorrelationScore_scaled.jpeg
data/results/figures/densityPlots_CorrelationScore_scaled_Melanoma_Psoriasis.jpeg
data/results/figures/densityPlots_CorrelationScore_scaled_usecaseVsnoshortlist.jpeg
data/results/figures/disease_genes.pvalues.boxplots.jpeg
data/results/figures/predictedDrugs_ROC.jpeg
data/results/figures/spia_real_simulated_pvalues_violinplots_biocarta.jpeg
data/results/figures/spia_real_simulated_pvalues_violinplots_kegg.jpeg
data/results/figures/spia_real_simulated_pvalues_violinplots_reactome.jpeg
data/results/spia_output/pairwise_genesets_intersection.RData
data/results/spia_output/spia_biocarta_disease.RData
data/results/spia_output/spia_biocarta_disease_simulated.RData
data/results/spia_output/spia_biocarta_drug.RData
data/results/spia_output/spia_kegg_disease.RData
data/results/spia_output/spia_kegg_disease_nofilter.RData
data/results/spia_output/spia_kegg_disease_simulated.RData
data/results/spia_output/spia_kegg_drug.RData
data/results/spia_output/spia_reactome_disease.RData
data/results/spia_output/spia_reactome_disease_simulated.RData
data/results/spia_output/spia_reactome_drug.RData
data/spia_input/kgml/hsa00010.xml
data/spia_input/kgml/hsa00020.xml
data/spia_input/kgml/hsa00030.xml
data/spia_input/kgml/hsa00040.xml
data/spia_input/kgml/hsa00051.xml
data/spia_input/kgml/hsa00052.xml
data/spia_input/kgml/hsa00053.xml
data/spia_input/kgml/hsa00061.xml
data/spia_input/kgml/hsa00062.xml
data/spia_input/kgml/hsa00071.xml
data/spia_input/kgml/hsa00072.xml
data/spia_input/kgml/hsa00100.xml
data/spia_input/kgml/hsa00120.xml
data/spia_input/kgml/hsa00130.xml
data/spia_input/kgml/hsa00140.xml
data/spia_input/kgml/hsa00190.xml
data/spia_input/kgml/hsa00220.xml
data/spia_input/kgml/hsa00230.xml
data/spia_input/kgml/hsa00232.xml
data/spia_input/kgml/hsa00240.xml
data/spia_input/kgml/hsa00250.xml
data/spia_input/kgml/hsa00260.xml
data/spia_input/kgml/hsa00270.xml
data/spia_input/kgml/hsa00280.xml
data/spia_input/kgml/hsa00290.xml
data/spia_input/kgml/hsa00310.xml
data/spia_input/kgml/hsa00330.xml
data/spia_input/kgml/hsa00340.xml
data/spia_input/kgml/hsa00350.xml
data/spia_input/kgml/hsa00360.xml
data/spia_input/kgml/hsa00380.xml
data/spia_input/kgml/hsa00400.xml
data/spia_input/kgml/hsa00410.xml
data/spia_input/kgml/hsa00430.xml
data/spia_input/kgml/hsa00440.xml
data/spia_input/kgml/hsa00450.xml
data/spia_input/kgml/hsa00471.xml
data/spia_input/kgml/hsa00472.xml
data/spia_input/kgml/hsa00480.xml
data/spia_input/kgml/hsa00500.xml
data/spia_input/kgml/hsa00510.xml
data/spia_input/kgml/hsa00511.xml
data/spia_input/kgml/hsa00512.xml
data/spia_input/kgml/hsa00514.xml
data/spia_input/kgml/hsa00515.xml
data/spia_input/kgml/hsa00520.xml
data/spia_input/kgml/hsa00524.xml
data/spia_input/kgml/hsa00531.xml
data/spia_input/kgml/hsa00532.xml
data/spia_input/kgml/hsa00533.xml
data/spia_input/kgml/hsa00534.xml
data/spia_input/kgml/hsa00561.xml
data/spia_input/kgml/hsa00562.xml
data/spia_input/kgml/hsa00563.xml
data/spia_input/kgml/hsa00564.xml
data/spia_input/kgml/hsa00565.xml
data/spia_input/kgml/hsa00590.xml
data/spia_input/kgml/hsa00591.xml
data/spia_input/kgml/hsa00592.xml
data/spia_input/kgml/hsa00600.xml
data/spia_input/kgml/hsa00601.xml
data/spia_input/kgml/hsa00603.xml
data/spia_input/kgml/hsa00604.xml
data/spia_input/kgml/hsa00620.xml
data/spia_input/kgml/hsa00630.xml
data/spia_input/kgml/hsa00640.xml
data/spia_input/kgml/hsa00650.xml
data/spia_input/kgml/hsa00670.xml
data/spia_input/kgml/hsa00730.xml
data/spia_input/kgml/hsa00740.xml
data/spia_input/kgml/hsa00750.xml
data/spia_input/kgml/hsa00760.xml
data/spia_input/kgml/hsa00770.xml
data/spia_input/kgml/hsa00780.xml
data/spia_input/kgml/hsa00785.xml
data/spia_input/kgml/hsa00790.xml
data/spia_input/kgml/hsa00830.xml
data/spia_input/kgml/hsa00860.xml
data/spia_input/kgml/hsa00900.xml
data/spia_input/kgml/hsa00910.xml
data/spia_input/kgml/hsa00920.xml
data/spia_input/kgml/hsa00970.xml
data/spia_input/kgml/hsa00980.xml
data/spia_input/kgml/hsa00982.xml
data/spia_input/kgml/hsa00983.xml
data/spia_input/kgml/hsa01040.xml
data/spia_input/kgml/hsa01100.xml
data/spia_input/kgml/hsa01200.xml
data/spia_input/kgml/hsa01210.xml
data/spia_input/kgml/hsa01212.xml
data/spia_input/kgml/hsa01230.xml
data/spia_input/kgml/hsa01521.xml
data/spia_input/kgml/hsa01522.xml
data/spia_input/kgml/hsa01523.xml
data/spia_input/kgml/hsa01524.xml
data/spia_input/kgml/hsa02010.xml
data/spia_input/kgml/hsa03008.xml
data/spia_input/kgml/hsa03010.xml
data/spia_input/kgml/hsa03013.xml
data/spia_input/kgml/hsa03015.xml
data/spia_input/kgml/hsa03018.xml
data/spia_input/kgml/hsa03020.xml
data/spia_input/kgml/hsa03022.xml
data/spia_input/kgml/hsa03030.xml
data/spia_input/kgml/hsa03040.xml
data/spia_input/kgml/hsa03050.xml
data/spia_input/kgml/hsa03060.xml
data/spia_input/kgml/hsa03320.xml
data/spia_input/kgml/hsa03410.xml
data/spia_input/kgml/hsa03420.xml
data/spia_input/kgml/hsa03430.xml
data/spia_input/kgml/hsa03440.xml
data/spia_input/kgml/hsa03450.xml
data/spia_input/kgml/hsa03460.xml
data/spia_input/kgml/hsa04010.xml
data/spia_input/kgml/hsa04012.xml
data/spia_input/kgml/hsa04014.xml
data/spia_input/kgml/hsa04015.xml
data/spia_input/kgml/hsa04020.xml
data/spia_input/kgml/hsa04022.xml
data/spia_input/kgml/hsa04024.xml
data/spia_input/kgml/hsa04060.xml
data/spia_input/kgml/hsa04062.xml
data/spia_input/kgml/hsa04064.xml
data/spia_input/kgml/hsa04066.xml
data/spia_input/kgml/hsa04068.xml
data/spia_input/kgml/hsa04070.xml
data/spia_input/kgml/hsa04071.xml
data/spia_input/kgml/hsa04072.xml
data/spia_input/kgml/hsa04080.xml
data/spia_input/kgml/hsa04110.xml
data/spia_input/kgml/hsa04114.xml
data/spia_input/kgml/hsa04115.xml
data/spia_input/kgml/hsa04120.xml
data/spia_input/kgml/hsa04122.xml
data/spia_input/kgml/hsa04130.xml
data/spia_input/kgml/hsa04136.xml
data/spia_input/kgml/hsa04137.xml
data/spia_input/kgml/hsa04140.xml
data/spia_input/kgml/hsa04141.xml
data/spia_input/kgml/hsa04142.xml
data/spia_input/kgml/hsa04144.xml
data/spia_input/kgml/hsa04145.xml
data/spia_input/kgml/hsa04146.xml
data/spia_input/kgml/hsa04150.xml
data/spia_input/kgml/hsa04151.xml
data/spia_input/kgml/hsa04152.xml
data/spia_input/kgml/hsa04210.xml
data/spia_input/kgml/hsa04211.xml
data/spia_input/kgml/hsa04213.xml
data/spia_input/kgml/hsa04215.xml
data/spia_input/kgml/hsa04216.xml
data/spia_input/kgml/hsa04217.xml
data/spia_input/kgml/hsa04218.xml
data/spia_input/kgml/hsa04260.xml
data/spia_input/kgml/hsa04261.xml
data/spia_input/kgml/hsa04270.xml
data/spia_input/kgml/hsa04310.xml
data/spia_input/kgml/hsa04330.xml
data/spia_input/kgml/hsa04340.xml
data/spia_input/kgml/hsa04350.xml
data/spia_input/kgml/hsa04360.xml
data/spia_input/kgml/hsa04370.xml
data/spia_input/kgml/hsa04371.xml
data/spia_input/kgml/hsa04380.xml
data/spia_input/kgml/hsa04390.xml
data/spia_input/kgml/hsa04392.xml
data/spia_input/kgml/hsa04510.xml
data/spia_input/kgml/hsa04512.xml
data/spia_input/kgml/hsa04514.xml
data/spia_input/kgml/hsa04520.xml
data/spia_input/kgml/hsa04530.xml
data/spia_input/kgml/hsa04540.xml
data/spia_input/kgml/hsa04550.xml
data/spia_input/kgml/hsa04610.xml
data/spia_input/kgml/hsa04611.xml
data/spia_input/kgml/hsa04612.xml
data/spia_input/kgml/hsa04614.xml
data/spia_input/kgml/hsa04620.xml
data/spia_input/kgml/hsa04621.xml
data/spia_input/kgml/hsa04622.xml
data/spia_input/kgml/hsa04623.xml
data/spia_input/kgml/hsa04625.xml
data/spia_input/kgml/hsa04630.xml
data/spia_input/kgml/hsa04640.xml
data/spia_input/kgml/hsa04650.xml
data/spia_input/kgml/hsa04657.xml
data/spia_input/kgml/hsa04658.xml
data/spia_input/kgml/hsa04659.xml
data/spia_input/kgml/hsa04660.xml
data/spia_input/kgml/hsa04662.xml
data/spia_input/kgml/hsa04664.xml
data/spia_input/kgml/hsa04666.xml
data/spia_input/kgml/hsa04668.xml
data/spia_input/kgml/hsa04670.xml
data/spia_input/kgml/hsa04672.xml
data/spia_input/kgml/hsa04710.xml
data/spia_input/kgml/hsa04713.xml
data/spia_input/kgml/hsa04714.xml
data/spia_input/kgml/hsa04720.xml
data/spia_input/kgml/hsa04721.xml
data/spia_input/kgml/hsa04722.xml
data/spia_input/kgml/hsa04723.xml
data/spia_input/kgml/hsa04724.xml
data/spia_input/kgml/hsa04725.xml
data/spia_input/kgml/hsa04726.xml
data/spia_input/kgml/hsa04727.xml
data/spia_input/kgml/hsa04728.xml
data/spia_input/kgml/hsa04730.xml
data/spia_input/kgml/hsa04740.xml
data/spia_input/kgml/hsa04742.xml
data/spia_input/kgml/hsa04744.xml
data/spia_input/kgml/hsa04750.xml
data/spia_input/kgml/hsa04810.xml
data/spia_input/kgml/hsa04910.xml
data/spia_input/kgml/hsa04911.xml
data/spia_input/kgml/hsa04912.xml
data/spia_input/kgml/hsa04913.xml
data/spia_input/kgml/hsa04914.xml
data/spia_input/kgml/hsa04915.xml
data/spia_input/kgml/hsa04916.xml
data/spia_input/kgml/hsa04917.xml
data/spia_input/kgml/hsa04918.xml
data/spia_input/kgml/hsa04919.xml
data/spia_input/kgml/hsa04920.xml
data/spia_input/kgml/hsa04921.xml
data/spia_input/kgml/hsa04922.xml
data/spia_input/kgml/hsa04923.xml
data/spia_input/kgml/hsa04924.xml
data/spia_input/kgml/hsa04925.xml
data/spia_input/kgml/hsa04926.xml
data/spia_input/kgml/hsa04927.xml
data/spia_input/kgml/hsa04928.xml
data/spia_input/kgml/hsa04930.xml
data/spia_input/kgml/hsa04931.xml
data/spia_input/kgml/hsa04932.xml
data/spia_input/kgml/hsa04933.xml
data/spia_input/kgml/hsa04934.xml
data/spia_input/kgml/hsa04940.xml
data/spia_input/kgml/hsa04950.xml
data/spia_input/kgml/hsa04960.xml
data/spia_input/kgml/hsa04961.xml
data/spia_input/kgml/hsa04962.xml
data/spia_input/kgml/hsa04964.xml
data/spia_input/kgml/hsa04966.xml
data/spia_input/kgml/hsa04970.xml
data/spia_input/kgml/hsa04971.xml
data/spia_input/kgml/hsa04972.xml
data/spia_input/kgml/hsa04973.xml
data/spia_input/kgml/hsa04974.xml
data/spia_input/kgml/hsa04975.xml
data/spia_input/kgml/hsa04976.xml
data/spia_input/kgml/hsa04977.xml
data/spia_input/kgml/hsa04978.xml
data/spia_input/kgml/hsa04979.xml
data/spia_input/kgml/hsa05010.xml
data/spia_input/kgml/hsa05012.xml
data/spia_input/kgml/hsa05014.xml
data/spia_input/kgml/hsa05016.xml
data/spia_input/kgml/hsa05020.xml
data/spia_input/kgml/hsa05030.xml
data/spia_input/kgml/hsa05031.xml
data/spia_input/kgml/hsa05032.xml
data/spia_input/kgml/hsa05033.xml
data/spia_input/kgml/hsa05034.xml
data/spia_input/kgml/hsa05100.xml
data/spia_input/kgml/hsa05110.xml
data/spia_input/kgml/hsa05120.xml
data/spia_input/kgml/hsa05130.xml
data/spia_input/kgml/hsa05131.xml
data/spia_input/kgml/hsa05132.xml
data/spia_input/kgml/hsa05133.xml
data/spia_input/kgml/hsa05134.xml
data/spia_input/kgml/hsa05140.xml
data/spia_input/kgml/hsa05142.xml
data/spia_input/kgml/hsa05143.xml
data/spia_input/kgml/hsa05144.xml
data/spia_input/kgml/hsa05145.xml
data/spia_input/kgml/hsa05146.xml
data/spia_input/kgml/hsa05150.xml
data/spia_input/kgml/hsa05152.xml
data/spia_input/kgml/hsa05160.xml
data/spia_input/kgml/hsa05161.xml
data/spia_input/kgml/hsa05162.xml
data/spia_input/kgml/hsa05164.xml
data/spia_input/kgml/hsa05165.xml
data/spia_input/kgml/hsa05166.xml
data/spia_input/kgml/hsa05167.xml
data/spia_input/kgml/hsa05168.xml
data/spia_input/kgml/hsa05169.xml
data/spia_input/kgml/hsa05200.xml
data/spia_input/kgml/hsa05202.xml
data/spia_input/kgml/hsa05203.xml
data/spia_input/kgml/hsa05204.xml
data/spia_input/kgml/hsa05205.xml
data/spia_input/kgml/hsa05206.xml
data/spia_input/kgml/hsa05210.xml
data/spia_input/kgml/hsa05211.xml
data/spia_input/kgml/hsa05212.xml
data/spia_input/kgml/hsa05213.xml
data/spia_input/kgml/hsa05214.xml
data/spia_input/kgml/hsa05215.xml
data/spia_input/kgml/hsa05216.xml
data/spia_input/kgml/hsa05217.xml
data/spia_input/kgml/hsa05218.xml
data/spia_input/kgml/hsa05219.xml
data/spia_input/kgml/hsa05220.xml
data/spia_input/kgml/hsa05221.xml
data/spia_input/kgml/hsa05222.xml
data/spia_input/kgml/hsa05223.xml
data/spia_input/kgml/hsa05224.xml
data/spia_input/kgml/hsa05225.xml
data/spia_input/kgml/hsa05226.xml
data/spia_input/kgml/hsa05230.xml
data/spia_input/kgml/hsa05231.xml
data/spia_input/kgml/hsa05310.xml
data/spia_input/kgml/hsa05320.xml
data/spia_input/kgml/hsa05321.xml
data/spia_input/kgml/hsa05322.xml
data/spia_input/kgml/hsa05323.xml
data/spia_input/kgml/hsa05330.xml
data/spia_input/kgml/hsa05332.xml
data/spia_input/kgml/hsa05340.xml
data/spia_input/kgml/hsa05410.xml
data/spia_input/kgml/hsa05412.xml
data/spia_input/kgml/hsa05414.xml
data/spia_input/kgml/hsa05416.xml
data/spia_input/kgml/hsa05418.xml
data/spia_input/lfc_2_disease_genes.RData
data/spia_input/lfc_disease_genes.RData
data/spia_input/lfc_disease_genes_namedVector.RData
data/spia_input/lfc_drugPdisease_ensembl_namedVector.RData
data/spia_input/lfc_drugPdisease_entrezID_namedVector.RData
data/spia_input/lfc_drugPdisease_entrez_namedVector.RData
data/spia_input/real_biocarta/hsaSPIA.RData
data/spia_input/real_kegg/hsaSPIA.RData
data/spia_input/real_react/hsaSPIA.RData
data/spia_input/simulated_biocarta/hsaSPIA.RData
data/spia_input/simulated_react/hsaSPIA.RData
data/stopgap.gene.mesh.RData
data/usecase_drugs.RData
notebooks/chemblid2name.ipynb
notebooks/creeds_loader.ipynb
notebooks/gsea_alternative.ipynb
ps4dr.Rproj
ps4dr.sh
