Man pages for PNNL-CompBio/amlresistancenetworks
Calculates networks that lead to AML resistance to drugs
| 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 |
