BMI_data                This function returns BMI data that comes form
                        the data in "Comparing tuberculosis gene
                        signatures in malnourished individuals using
                        the TBSignatureProfiler" paper. Subject IDs
                        were matched as shown on
                        "github.com/jessmcc22/BatchQCv2_Manuscript/blob/devel/R/subjectID_match.R"
BatchQC                 Run BatchQC shiny app
ComBat_correction       ComBat Correction This function applies ComBat
                        correction to your summarized experiment object
ComBat_seq_correction   ComBat-Seq Correction This function applies
                        ComBat-seq correction to your summarized
                        experiment object
DESeq2_small_size       This function calculated the goodness of fit of
                        DESeq2 for small sample sizes (intended for
                        less than 20 samples).
DESeq_large_analysis    This function calculated the goodness of fit of
                        DESeq2 for larger sample sizes (intended for
                        more than 20 samples).
DE_analyze              Differential Expression Analysis
EV_plotter              This function allows you to plot explained
                        variation
EV_table                EV Table Returns table with percent variation
                        explained for specified number of genes
PCA_plotter             This function allows you to plot PCA
batch_correct           Batch Correct This function allows you to Add
                        batch corrected count matrix to the SE object
batch_design            This function allows you to make a batch design
                        matrix
batch_indicator         Batch and Condition indicator for signature
                        data
batchqc_explained_variation
                        Returns a list of explained variation by batch
                        and condition combinations
bisect                  bisect - a generic bisection function
bladder_data_upload     Bladder data upload This function uploads the
                        Bladder data set from the bladderbatch package.
                        This dataset is from bladder cancer data with
                        22,283 different microarray gene expression
                        data. It has 57 bladder samples with 3 metadata
                        variables (batch, outcome and cancer). It
                        contains 5 batches, 3 cancer types (cancer,
                        biopsy, control), and 5 outcomes (Biopsy, mTCC,
                        sTCC-CIS, sTCC+CIS, and Normal). Batch 1
                        contains only cancer, 2 has cancer and
                        controls, 3 has only controls, 4 contains only
                        biopsy, and 5 contains cancer and biopsy
check_valid_input       Helper function to save variables as factors if
                        not already factors
color_palette           Color palette
commentary              This function creates the commentary
                        recommendation when there are more than 20
                        samples.
compute_aic             Compute the AIC for lognormal (ComBat) model,
                        negative binomial (ComBat-seq) model and the
                        Voom model
compute_lambda          Compute the lambda index for determining a need
                        for batch correction
confound_metrics        Combine std. Pearson correlation coefficient
                        and Cramer's V
cor_props               This function allows you to calculate
                        correlation properties
covariates_not_confounded
                        Returns list of covariates not confounded by
                        batch; helper function for explained variation
                        and for populating shiny app condition options
cramers_v               This function allows you to calculate Cramer's
                        V
dendrogram_alpha_numeric_check
                        Dendrogram alpha or numeric checker
dendrogram_color_palette
                        Dendrogram color palette
dendrogram_plotter      Dendrogram Plot
get.res                 Helper function to get residuals
goodness_of_fit_DESeq2
                        This function calculates goodness-of-fit
                        pvalues for all genes by looking at how the NB
                        model by DESeq2 fit the data
heatmap_num_to_char_converter
                        Heatmap numeric to character converter
heatmap_plotter         Heatmap Plotter
is_design_balanced      Check if the experimental design is balanced or
                        unbalanced
kBET                    kBET - k-nearest neighbour batch effect test
limma_correction        Limma Correction This function applies limma
                        batch correction to your provided assay
merged_IDs              BMI and matched sample names for TB data
nb_histogram            This function creates a histogram from the
                        negative binomial goodness-of-fit adjusted
                        pvalues.
nb_proportion           This function determines the proportion of
                        p-values below a specific value and compares to
                        the previously determined threshold of 0.42 for
                        extreme low values.
normalize_SE            This function allows you to add normalized
                        count matrix to the SE object
permuted_DESeq          This function performs DESeq on the permuted
                        dataset adjusted pvalues.
plot_data               This function formats the PCA plot using ggplot
plot_kBET               kBET Rejection Plotter
possible_distances      Create potential min_distance values for
                        exploratory analysis based on the value of
                        spread
possible_k_neighbors    Create a vector of possible nearest neighbor
                        values from 5, 15, 25, 50, and 100
preprocess              Preprocess assay data
process_dendrogram      Process Dendrogram
protein_data            Protein data with 39 protein expression levels
protein_sample_info     Batch and Condition indicator for protein
                        expression data
pval_plotter            P-value Plotter This function allows you to
                        plot p-values of explained variation
pval_summary            Returns summary table for p-values of explained
                        variation
ratio_plotter           This function allows you to plot ratios of
                        explained variation
run_kBET                kBET rejection rate
run_lambda              Provide a recommendation on batch correction
                        based on lambda calculation
signature_data          Signature data with 1600 gene expression levels
std_pearson_corr_coef   Calculate a standardized Pearson correlation
                        coefficient
summarized_experiment   This function creates a summarized experiment
                        object from count and metadata files uploaded
                        by the user
sva_correction          sva Correction This function applies sva
                        correction to a summarized experiment object
                        (implementation adapted from sva::psva)
svaseq_correction       svaseq Correction This function applies sva
                        correction to a summarized experiment object
                        with count based RNA-seq data
tb_data_upload          TB data upload This function uploads the TB
                        data set from the curatedTBData package.
umap                    Create a umap plot; wrapper function for umap
                        package plus custom plotting
variation_ratios        Creates Ratios of batch to variable variation
                        statistic
volcano_plot            Volcano plot
