Man pages for TBSignatureProfiler
Profile RA-Seq Data Using TB Pathway Signatures
| bootstrapAUC | Bootstrap the AUC and conduct T-Tests for a collection of... |
| Bootstrap_LOOCV_LR_AUC | Bootstrap on Leave-one-out CV with Logistic Regression. |
| common_sigAnnotData | Annotation information for published TB signatures. |
| compareAlgs | Compare scoring algorithms on a single signature via heatmap... |
| compareBoxplots | Create a comparison plot of boxplots for bootstrapped AUC... |
| deseq2_norm_rle | Normalize gene expression count data. |
| distinctColors | Generate a distinct palette for coloring different clusters. |
| LOOAUC_simple_multiple_noplot_one_df | Perform Leave-one-out CV with Logistic Regression. |
| mkAssay | Add SummarizedExperiment assays to the data structure. |
| plotQuantitative | Create a boxplot using logistic regression and bootstrap... |
| runTBsigProfiler | Run TB gene signature profiling. |
| sigAnnotData | Annotation information for published TB signatures. |
| signatureBoxplot | Plot a boxplot of signature genes. |
| signatureGeneHeatmap | Plot a heatmap of a single signature score with individual... |
| signatureHeatmap | Plot a heatmap of signature scores. |
| SignatureQuantitative | Use logistic regression and bootstrap LOOCV to evaluate... |
| signatureROCplot | Create an array of ROC plots to compare signatures. |
| signatureROCplot_CI | Create an array of ROC plots with confidence interval bands... |
| tableAUC | Create a table of results for t-tests and bootstrapped AUCs... |
| TBcommon | A list of published TB signatures, using author-given names. |
| TB_hiv | An example TB dataset with TB/HIV data. |
| TB_indian | An example TB dataset with Indian population data. |
| TBsignatures | A list of published TB signatures. |
| TBSPapp | Run the TBSignatureProfiler Shiny application. |
