.OriginalModel_NoRetraining
                        TB gene signatures that do not require
                        retraining.
.OriginalModel_Retraining
                        TB gene signatures that require retraining.
Bootstrap_LOOCV_LR_AUC
                        Bootstrap on Leave-one-out CV with Logistic
                        Regression.
COVIDsignatures         A list of published/pre-print COVID-19
                        signatures.
LOOAUC_simple_multiple_noplot_one_df
                        Perform Leave-one-out CV with Logistic
                        Regression.
ObtainSampleScore_OriginalModel
                        Obtain training data, testing data, and train
                        signature's original model.
OriginalTrainingData    Discovery datasets for corresponding gene
                        signatures.
SignatureQuantitative   Use logistic regression and bootstrap LOOCV to
                        evaluate signatures.
SulimanOriginalModel    Train original model gene signature
                        Suliman_RISK_4.
TBSPapp                 Run the TBSignatureProfiler Shiny application.
TB_hiv                  An example TB dataset with TB/HIV data.
TB_indian               An example TB dataset with Indian population
                        data.
TBcommon                A list of published TB signatures, using
                        author-given names.
TBsignatures            A list of published TB signatures.
TBsignaturesSplit       Up/Down-regulated genes information for
                        selected TB signatures.
addTBsignature          Introduce a new signature into the
                        TBSignatureProfiler.
bootstrapAUC            Bootstrap the AUC and conduct T-Tests for a
                        collection of signatures.
common_sigAnnotData     Annotation information for published TB
                        signatures.
compareAlgs             Compare scoring algorithms on a single
                        signature via heatmap or boxplot.
compareBoxplots         Create a comparison plot of boxplots for
                        bootstrapped AUC values.
cv_glmnet_OriginalModel
                        Train original model for gene signatures
                        Leong_24, Leong_RISK_29, Zhao_NANO_6 using
                        lasso logistic regression.
deseq2_norm_rle         Normalize gene expression count data.
distinctColors          Generate a distinct palette for coloring
                        different clusters.
evaluateOriginalModel   A function that implements the original methods
                        for multiple TB signatures.
knn_OriginalModel       Train original model for gene signatures
                        Berry_393 and Berry_OD_86.
lda_OriginalModel       Train original model for gene signatures
                        Jacobsen_3 and Sambarey_HIV_10.
mkAssay                 Add SummarizedExperiment assays to the data
                        structure.
plotQuantitative        Create a boxplot using logistic regression and
                        bootstrap LOOCV to evaluate signatures.
randomForest_OriginalModel
                        Train original model for gene signatures
                        Maertzdorf_4, Maertzdorf_15, Verhagen_10, and
                        LauxdaCosta_OD_3.
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 gene expression levels.
signatureHeatmap        Plot a heatmap of signature scores.
signatureROCplot        Create an array of ROC plots to compare
                        signatures.
signatureROCplot_CI     Create an array of ROC plots with confidence
                        interval bands to compare signatures.
subsetGeneSet           Filter gene expression value matrix based on
                        certain gene sets.
svm_OriginalModel       Train original model for gene signatures
                        Bloom_OD_144 and Zak_RISK_16.
tableAUC                Create a table of results for t-tests and
                        bootstrapped AUCs for multiple scored
                        signatures.
