buildFeatureMatrix | buildFeatureMatrix This function sits at the core of the... |
clusterDrugFamilyEfficacy | selects AUC data and molecular data nand builds heatmap of... |
clusterSingleDrugEfficacy | selects AUC data and molecular data nand builds heatmap of... |
computeAUCCorVals | what molecules are |
computeDiffExByDrug | Nots ure if this is used yet Currently deprecated |
computeFoldChangePvals | Reads in data frame and computes fold change |
computeGSEA | compute gene set enrichment - osama's code wrapped in... |
computeKSEA | compute kinase substrate enrichment - osama's code wrapped in... |
computePhosphoChanges | get ordered phospho sites |
computePhosphoNetwork | computePhosphoNetwork maps kinase activity to proteins in a... |
computeProteinNetwork | computeProteinNetwork |
doRegularGo | Runs regular bag of genes enrichment |
doRegularKin | Runs regular bag of genes enrichment |
drugMolLogReg | drugMolLogReg Computes logistic regression based on AUC... |
drugMolLogRegEval | drugMolLogRegEval Computes logistic regression and evaluates... |
drugMolRandomForest | drugMolRandomForest builds random forest predictor of... |
drugMolRegression | working on this function still The goal is to use a basic... |
drugMolRegressionEval | drugMolRegressionEval This is the primary function that runs... |
findCandidates | The goal is to pre filter features using limma, with the hope... |
getCoClusteredProteins | getCoClusteredProteins Designed to evaluate time-course data... |
getCorrelatedProteins | Get correlated proteins Computes protein correlations with... |
getCytokineSensData | getCytokine data gets cytokine sensitivity data and metadata... |
getFeaturesFromString | getFeaturesFromString - separates out comma-delimited model... |
getFeaturesFromStringdf | getFeaturesFromStringdf - separates out comma-delimited model... |
getTimeCourseData | getTimecourseData |
limmaTwoFactorDEAnalysis | limmaTwoFactorDEAnalysis uses Osama's code to compute de from... |
manualDEAnalysis | compute manual lfc |
mapPhosphoToKinase | mapPhosphoToKInase reads in phospho data, looads of KSDB and... |
miniForest | miniForest Runds random forest on the table and molecular... |
miniForestEval | miniForestEval |
miniLogR | miniDE Carries out differential expressiona nalysis using an... |
miniLogREval | miniLogReval: Assesses the performance of building a logistic... |
miniReg | miniReg Runs lasso regression on a single feature from... |
miniRegEval | miniRegEval Runs lasso regression on a single feature from... |
plotAllAUCs | plotall AUCS with clinical data what are we measuring here |
plotCorrelationEnrichment | Plot using correlation enrichment from leapR package. A... |
plotCorrelationsByDrug | how do we visualize the correlations of each drug/gene pair? |
plotGSEA | Plot using clusterProfiler. 3 GSEA plots are saved to the... |
plotKinDat | plotKinDat |
plotOldGSEA | Plot using clusterProfiler. 3 GSEA plots are saved to the... |
plotProtsByMetric | plotPRotsByMetric plots basal protein expression by metric... |
plotSingleProtein | plot single protein |
querySynapseTable | query synapse table This is how you get data from the project |
readAndTidyMetadata | reads in metadata from excel spreadsheet and tidies it |
readAndTidyPhosphoProtMeasures | reads and tidies phosphoprotein measurements joins with... |
readAndTidyProtMeasures | reads and tidies protein measurements joins with metadata... |
readAndTidyQuizMetadata | reads in metadata from excel spreadsheet and tidies it |
readAndTidyQuizPhosphoProtMeasures | reads and tidies phosphoprotein measurements joins with... |
readAndTidyQuizProtMeasures | reads and tidies protein measurements joins with metadata... |
readAndTidySensMetadata | reads and tidies experiment 11 metadata |
readAndTidySensPhosMeasures | reads and tidies phosphototeomic data for experimnet 11 |
readAndTidySensProtMeasure | reads and tidies bulk proteomic data for experiment 11 |
readAndTidyUncorrectedQuizPhosphoMeasures | reads and tidies uncorrected phosphoprotein measurements... |
reverselog_trans | Used to make reversed logarithmic scales |
synapseLogin | Logs into Synapse using local information |
synapseStore | Synapse store |
synTableStore | Synapse table store REQUIRES PANDAS ON YOUR PYTHON PATH |
synTableUpdate | synTableUpdate Removes all rows from table and replaces |
testData | testData |
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