Man pages for momeara/MPStats
Tools for analyzing Morphological Profiling data
| bayesplot_theme | Set bayesplot theme to MPStat defaults |
| binomial_quantile | Quantile of bayesian estimator for binomial trial with flat... |
| binomial_variance | Variance of Bayesian estimator for binomial trial with flat... |
| compute_qc_covariates | Compute important quality control covariates suggested by... |
| date_code | create date code of the form YYYYMMDD inputs: d (optional):... |
| fit_brms_flat_score_by_dose | brms flat model for score by compound dose |
| fit_brms_hill_score_by_dose | brms hill model for score by compound dose |
| fit_brms_npos_nneg_by_dose | brms model for the counts of positive and negative cells by... |
| fit_drc_score_by_dose | DRC 4-param dose response fits with bottom fixed = 0 |
| fit_MuSyC_score_by_dose | Fit the MuSyC synergy model by dose |
| fit_MuSyC_score_by_dose_robust | Combined: sample1 = |
| fit_principal_curves | fit principle curves |
| generate_hill_effects | Simulate hill model from the parameters |
| generate_MuSyC_effects | Drug Synergy MuSyC Drug Synergy model |
| generate_MuSyC_effects_robust | Generate MuSyC Ed scores using a robust functional form It... |
| GeomIndicator | ggplot2 geom that adds a label to facet panes |
| get_database_connection | Construct a database from database connection parameters |
| loo_R2_indicator | Summarize the loo_R2 as a plot indicator |
| model_cell_count_by_batch_vars_lm | Model cell count by batch variables using a linear model |
| model_score_by_batch_vars_lm | Model score by batch variables using a weighted least squares... |
| MuSyC_default_prior | Default priors for MuSyC synergy model |
| MuSyC_hi_to_si | Convert from slope parametrization to the exponent... |
| MuSyC_si_to_hi | Convert from slope parametrization to the exponent... |
| pairsplot | Customized pairs plot |
| plate_layout | get plate layout |
| plot_binomial_variance_by_cell_count | A diagnostic plot for error analysis for binomial trials |
| plot_brms_predictor_residual_score_by_dose | Plot the score as a function of compound dose for brms models |
| plot_brms_score_by_dose | Plot the score as a function of compound dose for brms models |
| plot_cell_count_by_batch_vars_density | plot cell count by batch variables as a density plot |
| plot_cell_count_by_batch_vars_scatter | plot cell count by batch variables as a scatterplot |
| plot_checkerboard_score_by_dose | Plot dose-response checkerboard |
| plot_drc_score_by_dose | Plot the score as a function of compound dose |
| plot_embedded_cluster_principal_curves | Plot embedded cluster principal cluves |
| plot_heatmap | plot feature heatmap |
| plot_principal_curve_projections | Plot embedded cluster principal cluves |
| plot_score_by_batch_vars_density | plot cell count by batch variables as a density plot |
| plot_score_by_batch_vars_scatter | plot cell count by batch variables as a scatter plot |
| plot_score_by_cell_count | plot score by cell count |
| plot_Zprime_by_dye | Plot Zprime score by Dye combination |
| plot_Zprime_by_top_features | Plot Zprime by top features |
| poisson_quantile | Quantile of bayesian estimators for samples of a poisson... |
| populate_cds | Popluate a Monocle3 cell data set from cell features |
| prior_posterior_plot | Create a plot that compares the distribution of prior and... |
| rankplot | Customized rank plot |
| read_cell_features | Read cell features |
| read_compound_moa | Read compound mechanism of action table |
| read_well_scores | Read well scores table |
| read_Zprime_by_plate | Read Zprime by plate |
| serialize_clusters | Write out clusters from monocle3 cell dataset |
| traceplot | Customized trace plot |
| umich_colors | Univrsity of Michigan colors |
| well_id_to_column | Extract column index from well identifier |
| well_id_to_row | Extract row index from well identifier |
| well_index_to_column | Extract column index from well index |
| well_index_to_row | Extract row index from well index |
| Zprime | Compute Zprime score |
