clip_matrix_values      Clip matrix values to specified range
close_progress_bar      Close progress bar
compare_expression      Compare gene expression between two groups
correct                 Correct data by setting all latent factors to
                        their median values and reversing the
                        regression model
correct_counts          Correct data by setting all latent factors to
                        their median values and reversing the
                        regression model
diff_mean_test          Non-parametric differential expression test for
                        sparse non-negative data
diff_mean_test_conserved
                        Find differentially expressed genes that are
                        conserved across samples
generate                Generate data from regularized models.
get_model_formula       Extract model formula from model string
get_model_var           Return average variance under negative binomial
                        model
get_nz_median2          Get median of non zero UMIs from a count matrix
get_residual_var        Return variance of residuals of regularized
                        models
get_residuals           Return Pearson or deviance residuals of
                        regularized models
is_outlier              Identify outliers
make.sparse             Convert a given matrix to dgCMatrix
pbmc                    Peripheral Blood Mononuclear Cells (PBMCs)
plot_model              Plot observed UMI counts and model
plot_model_pars         Plot estimated and fitted model parameters
prepare_regressor_data
                        Prepare regressor data from vst object and cell
                        attributes
robust_scale            Robust scale using median and mad
robust_scale_binned     Robust scale using median and mad per bin
row_gmean               Geometric mean per row
row_var                 Variance per row
setup_progress_bar      Setup progress bar for batch processing
smooth_via_pca          Smooth data by PCA
umify                   Quantile normalization of cell-level data to
                        match typical UMI count data
umify_data              Transformation functions for umify
update_progress_bar     Update progress bar
vst                     Variance stabilizing transformation for UMI
                        count data
