Man pages for TBSignatureProfiler
Profile RA-Seq Data Using TB Pathway Signatures

bootstrapAUCBootstrap the AUC and conduct T-Tests for a collection of...
Bootstrap_LOOCV_LR_AUCBootstrap on Leave-one-out CV with Logistic Regression.
common_sigAnnotDataAnnotation information for published TB signatures.
compareAlgsCompare scoring algorithms on a single signature via heatmap...
compareBoxplotsCreate a comparison plot of boxplots for bootstrapped AUC...
deseq2_norm_rleNormalize gene expression count data.
distinctColorsGenerate a distinct palette for coloring different clusters.
LOOAUC_simple_multiple_noplot_one_dfPerform Leave-one-out CV with Logistic Regression.
mkAssayAdd SummarizedExperiment assays to the data structure.
plotQuantitativeCreate a boxplot using logistic regression and bootstrap...
runTBsigProfilerRun TB gene signature profiling.
sigAnnotDataAnnotation information for published TB signatures.
signatureBoxplotPlot a boxplot of signature genes.
signatureGeneHeatmapPlot a heatmap of a single signature score with individual...
signatureHeatmapPlot a heatmap of signature scores.
SignatureQuantitativeUse logistic regression and bootstrap LOOCV to evaluate...
signatureROCplotCreate an array of ROC plots to compare signatures.
signatureROCplot_CICreate an array of ROC plots with confidence interval bands...
tableAUCCreate a table of results for t-tests and bootstrapped AUCs...
TBcommonA list of published TB signatures, using author-given names.
TB_hivAn example TB dataset with TB/HIV data.
TB_indianAn example TB dataset with Indian population data.
TBsignaturesA list of published TB signatures.
TBSPappRun the TBSignatureProfiler Shiny application.
TBSignatureProfiler documentation built on Nov. 8, 2020, 6:56 p.m.