Man pages for dfjenkins3/TBSignatureProfiler
Profile RNA-Seq Data Using TB Pathway Signatures
| addTBsignature | Introduce a new signature into the TBSignatureProfiler. |
| 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... |
| COVIDsignatures | A list of published/pre-print COVID-19 signatures. |
| cv_glmnet_OriginalModel | Train original model for gene signatures Leong_24,... |
| deseq2_norm_rle | Normalize gene expression count data. |
| distinctColors | Generate a distinct palette for coloring different clusters. |
| dot-OriginalModel_NoRetraining | TB gene signatures that do not require retraining. |
| dot-OriginalModel_Retraining | TB gene signatures that require retraining. |
| evaluateOriginalModel | A function that implements the original methods for multiple... |
| knn_OriginalModel | Train original model for gene signatures Berry_393 and... |
| lda_OriginalModel | Train original model for gene signatures Jacobsen_3 and... |
| LOOAUC_simple_multiple_noplot_one_df | Perform Leave-one-out CV with Logistic Regression. |
| mkAssay | Add SummarizedExperiment assays to the data structure. |
| ObtainSampleScore_OriginalModel | Obtain training data, testing data, and train signature's... |
| OriginalTrainingData | Discovery datasets for corresponding gene signatures. |
| plotQuantitative | Create a boxplot using logistic regression and bootstrap... |
| randomForest_OriginalModel | Train original model for gene signatures Maertzdorf_4,... |
| ref_combat_impute | A function for reference batch correction and imputation. |
| 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... |
| subsetGeneSet | Filter gene expression value matrix based on certain gene... |
| SulimanOriginalModel | Train original model gene signature Suliman_RISK_4. |
| svm_OriginalModel | Train original model for gene signatures Bloom_OD_144 and... |
| 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. |
| TBsignaturesSplit | Up/Down-regulated genes information for selected TB... |
| TBSPapp | Run the TBSignatureProfiler Shiny application. |
