Man pages for sgosline/mpnstXenoModeling
MPNST Xenograft Modeling
| compress_enrichment | Plot using correlation enrichment from leapR package. A... |
| computeAUC | AUC - area under the curve computes difference between AUC of... |
| computeGRI | GRI - growth rate inhibition |
| computeTGI | TGI - tumor growth index |
| dataFromSynTable | gets a list of synapse ids and binds them together |
| deseq2NormFilter | deseq2NormFilter Utilizes the geometric mean to normalize the... |
| do_deseq_import | do_deseq2 import Uses tximport functionality to properly... |
| doGSEA | Old plot using clusterProfiler |
| doRegularGo | Runs regular bag of genes enrichment |
| drcmod | drcmod Modified dose response curve function |
| drugMutationsCor | drugMutationCor Evaluates correlation betwen allele depth and... |
| drugTranscriptCor | drugTranscriptCor Evaluates correlation |
| ds2FactorDE | ds2FactorDE |
| fixDrugData | fixDrugData |
| formatDataToXeva | formatDataToXeva |
| geneIdToSymbolMatrix | geneIdToSymbolMatrix This takes a symbol wtih gene ids and... |
| generate_DR_plots | generate_DR_plots We need to fit the data to a curve to plot |
| generate_TR_plots | generate_TR_plots |
| getAllDrugStats | getAllDrugStats |
| getMicroTissueDrugData | getMicroTissueDrugData |
| getNewSomaticCalls | getNewSomaticCalls james said this is the format for future... |
| hypothesisTestPlotsDE | #### Optional function to visualize hypothesis testing |
| limmaTwoFactorDEAnalysis | limmaTwoFactorDEAnalysis |
| loadIncucyteData | loadIncucyteData |
| loadMicrotissueDrugData | loadMicrotissueDrugData |
| loadMicrotissueMetadata | loadMicrotissueMetadata loads and stores microtissue metata... |
| loadPDXData | loadPDXData gets data from synapse and stores them as global... |
| loadPDXDrugData | loadPDXDrugData |
| loadRNASeqData | loadRNASeqData |
| loadVariantData | loadVariantData |
| normDiffEx | normDiffEx Normalizes differential data using limma and voom |
| parseSynidListColumn | parses a list of synapse ids, like form 'syn24215021' |
| plotCorrelationEnrichment | Plot using correlation enrichment from leapR package. A... |
| plotDrugData | plotHistogram of drug data |
| plotGenesetResults | ploGenesetResults Internal function to plot results of... |
| plotIncTreatmentByDrug | plotIncTreatmentByDrug |
| plotMTTreatmentByDrug | plotMTTreatmentByDrug |
| plotMTTreatmentBySample | plotMTTreatmentBySample |
| plotPDXTreatmentBySample | plotPDXTreatmentBySample |
| plotTopGenesHeatmap | plotTopGenesHeatmap |
| plotTumorGrowthCorrelations | plotTumorGrowthCorrelations |
| process_IncucyteDrugData | process_IncucyteDrugData |
| queryPartSynapseTable | query synapse table more selectively This is how you get data... |
| querySynapseTable | query synapse table This is how you get data from the project |
| reverselog_trans | Used to make reversed logarithmic scales |
| statsForDrugPatient | statsForDrugPatient |
| synapseLogin | Logs into Synapse using local information |
| synapseStore | Synapse store |
| synTableStore | Synapse table store REQUIRES PANDAS ON YOUR PYTHON PATH |
| tidiedTableToExpressionSet | This function takes a tidied table of data and makes into... |
| TryFit | TryFit Takes the dose response data and fits it to various... |
