cepip                   Run CEP-IP, optionally with SKCS and CMRF
cepip_associate         Donor-level association with outcomes
cepip_band              CMRF tolerance band (Stage 1)
cepip_cmrf              Copula monotone recovery filter (CMRF)
cepip_composite         Composite expression of partner genes
cepip_deg               Differential expression between cell groups,
                        paired by donor
cepip_donor             Per-donor share of cells in each group
cepip_ep                Cell explanatory power and TREP cells
cepip_example           Download the SEA-AD example data
cepip_example_clear     Delete the cached example data
cepip_fit               Fit the CEP-IP GAM
cepip_groups            Cell groups for downstream analyses
cepip_ip                Inflection point (IP) and IP reliability score
                        (IPRS)
cepip_save              Save the tables and plots of one arm
cepip_screen            Spearman-Kendall dual-filter screen for partner
                        genes
cepip_skcs              Spearman-Kendall cell-level scores (SKCS)
cepip_toy               Simulated example data
cepip_validate          Validate the CMRF Module by refitting the
                        CEP-IP GAM (Validation1)
plot_associate          Forest plot of donor-level associations
plot_band               Plot the formation of the CMRF band (Figure 6)
plot_copula             Plot the cells and the CMRF band in copula
                        space
plot_deg                Volcano plot of one differential expression
                        contrast
plot_donor              Plot the per-donor Module Post-IP percentage
plot_fit                Plot the CEP-IP GAM with the inflection point
plot_module             Pitcher plot of the CMRF classes in copula
                        space (Figure 8A)
plot_pitcher            Pitcher plot of the SKCS scores
plot_prss               Plot the PRSS search over the basis dimension k
plot_residual           Plot the residual GAM R(x) and the IP
plot_rskfcv             Plot the RSk-fCV gate of CMRF Stage 2 (Figure
                        7)
plot_screen             Plot the partner-gene screen of one GOI
plot_validate           Plot the Validation1 refit of the CMRF Module
print.cepip_figure      Draw a multi-panel cepip figure
