add_noise               Add noise to count data
adjust_library_size     Adjust count matrix by library size
cellMarkers             Identify cell markers
collapse_group          Collapse groups in cellMarkers object
comp_heatmap            Compensation heatmap
confint.deconv          Confidence Intervals for Deconvolution Models
cos_similarity          Gene signature cosine similarity matrix
deconvolute             Deconvolute bulk RNA-Seq using single-cell
                        RNA-Seq signature
diagnose                Diagnostics for cellMarker signatures
fix_bulk                Fix in missing genes in bulk RNA-Seq matrix
fix_group               Fix cellMarkers signature with no cell groups
gene2symbol             Converts ensembl gene ids to symbols
gene_angle              Vector based best marker selection
generate_samples        Generate random cell number samples
kappa.deconv            Compute condition number of deconvolution model
logmean                 Mean Objects
max_similarity          Maximum similarity between cell types
mergeMarkers            Merge cellMarker signatures
metric_set              Calculate R-squared and metrics on deconvoluted
                        cell subclasses
plot.qqmap              Quantile-quantile plot
plot_biasvar            Plot bias-variance decomposition
plot_comp               Plot compensation analysis
plot_cv                 Plot deconvolution lambda cross-validation
                        curve
plot_pred               Scatter plot to compare deconvoluted subclasses
plot_residuals          Residuals plot
plot_set                Scatter plots to compare deconvoluted
                        subclasses
plot_tune               Plot tuning curves
quantile_map            Quantile mapping function between two scRNA-Seq
                        datasets
rank_angle              Rank distance angles from a cosine similarity
                        matrix
reduceNoise             Reduce noise in single-cell data
residuals.deconv        Extract Deconvolution Residuals
rstudent.deconv         Regression Deletion Diagnostics
scapply                 Single-cell apply a function to a matrix split
                        by a factor
scmean                  Single-cell mean log gene expression across
                        cell types
se                      Standard errors of deconvoluted cell counts
signature_heatmap       Gene signature heatmap
simulate_bulk           Simulate pseudo-bulk RNA-Seq
slapply                 Apply a function to a big matrix by slicing
specificity_plot        Specificity plot
spillover_heatmap       Spillover heatmap
stack_plot              Stacked bar plot
summary.tune_deconv     Summarising deconvolution tuning
tune_deconv             Tune deconvolution parameters
updateMarkers           Update cellMarkers object
violin_plot             Cell subclass violin plot
