API for dmcable/RCTD
SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics
| Global functions | |
|---|---|
| CSIDE.population.inference | Man page Source code |
| RCTD-class | Man page |
| RCTD.replicates-class | Man page |
| Reference | Man page Source code |
| Reference-class | Man page |
| SpatialRNA | Man page Source code |
| SpatialRNA-class | Man page |
| UMI_cutoff | Source code |
| aggregate_cell_types | Man page Source code |
| bin_quant_df | Source code |
| build.designmatrix.intercept | Source code |
| build.designmatrix.nonparam | Man page Source code |
| build.designmatrix.regions | Man page Source code |
| build.designmatrix.single | Man page Source code |
| calc_Q_all | Source code |
| calc_Q_mat_one | Source code |
| calc_Q_par | Source code |
| calc_log_l_vec | Source code |
| calc_log_l_vec_fast | Source code |
| check_UMI | Source code |
| check_cell_type_specific | Source code |
| check_cell_types | Source code |
| check_converged_vec | Source code |
| check_coords | Source code |
| check_counts | Source code |
| check_designmatrix | Source code |
| check_pairs_type | Source code |
| check_vector | Source code |
| chooseSigma | Source code |
| chooseSigma2 | Source code |
| choose_cell_types | Source code |
| choose_sigma_c | Man page Source code |
| choose_sigma_gene | Source code |
| coerce_deglam_reference | Source code |
| coerce_old | Source code |
| construct_hess_fast | Source code |
| convert.old.RCTD | Man page Source code |
| convert_old_reference | Source code |
| count_cell_types | Man page Source code |
| create.RCTD | Man page Source code |
| create.RCTD.replicates | Man page Source code |
| create_RCTD_plots | Man page Source code |
| create_downsampled_data | Source code |
| decompose_batch | Source code |
| decompose_doublet_fast | Source code |
| decompose_full | Source code |
| decompose_sparse | Source code |
| estimate_effects_trust | Source code |
| estimate_gene_wrapper | Source code |
| estimate_tau | Source code |
| estimate_tau_group | Source code |
| export.RCTD | Source code |
| exvar.celltocell.interactions | Man page Source code |
| exvar.point.density | Man page Source code |
| fake_coords | Source code |
| fdr_sig_genes | Source code |
| filter_barcodes_cell_types | Source code |
| filter_genes | Source code |
| find_sig_genes_categorical | Source code |
| find_sig_genes_individual | Source code |
| fitBulk | Man page Source code |
| fitPixels | Man page Source code |
| fit_de_genes | Source code |
| gather_results | Source code |
| get_Q | Source code |
| get_Q_all | Source code |
| get_beta_doublet | Source code |
| get_beta_multi | Source code |
| get_cell_type_ind | Source code |
| get_cell_type_info | Man page Source code |
| get_class_df | Source code |
| get_con_regions | Source code |
| get_d1_d2 | Source code |
| get_de_gene_fits | Source code |
| get_de_genes | Man page Source code |
| get_de_pop | Source code |
| get_decomposed_data | Man page Source code |
| get_decomposed_data_full_doublet | Source code |
| get_der_fast | Source code |
| get_doublet_weights | Man page Source code |
| get_gene_list_type | Source code |
| get_gene_list_type_wrapper | Source code |
| get_l_chi | Source code |
| get_means_sds | Source code |
| get_norm_ref | Man page Source code |
| get_p_chi | Source code |
| get_p_qf | Source code |
| get_param_names | Source code |
| get_posterior_mean | Source code |
| get_prediction_sparse | Source code |
| get_quant_df | Source code |
| get_sig_genes | Source code |
| get_singlet_score | Source code |
| get_spline_matrix | Source code |
| get_standard_errors | Man page Source code |
| ht_pdf | Source code |
| ht_pdf_norm | Source code |
| import_weights | Man page Source code |
| likelihood_to_dist | Source code |
| make_all_de_plots | Man page Source code |
| make_de_plots_genes | Man page Source code |
| make_de_plots_predictions | Source code |
| make_de_plots_quant | Man page Source code |
| make_de_plots_regions | Man page Source code |
| make_de_plots_replicates | Man page Source code |
| make_de_plots_spatial | Man page Source code |
| merge_RCTD_objects | Man page Source code |
| mysweept | Source code |
| normalize_de_estimates | Source code |
| normalize_ev | Source code |
| normalize_weights | Man page Source code |
| one_ct_genes | Source code |
| plot_all_cell_types | Man page Source code |
| plot_class | Man page Source code |
| plot_cond_occur | Man page Source code |
| plot_doub_occur_stack | Man page Source code |
| plot_doublets | Man page Source code |
| plot_doublets_type | Man page Source code |
| plot_gene_raw | Man page Source code |
| plot_gene_regions | Man page Source code |
| plot_gene_two_regions | Man page Source code |
| plot_occur_unthreshold | Man page Source code |
| plot_prediction_gene | Man page Source code |
| plot_prediction_genes | Source code |
| plot_puck_continuous | Man page Source code |
| plot_puck_wrapper | Man page Source code |
| plot_quant_df | Source code |
| plot_sig_genes | Source code |
| plot_sig_genes_quant | Source code |
| plot_sig_genes_quant_regions | Source code |
| plot_sig_genes_regions | Source code |
| plot_sig_genes_two_regions | Source code |
| plot_weights | Man page Source code |
| plot_weights_doublet | Man page Source code |
| plot_weights_unthreshold | Man page Source code |
| predict_CSIDE | Source code |
| predict_CSIDE_all | Source code |
| prepareBulkData | Source code |
| process_bead_doublet | Source code |
| process_bead_multi | Source code |
| process_beads_batch | Man page Source code |
| process_beads_multi | Source code |
| process_cell_type_info | Source code |
| process_data | Man page Source code |
| psd | Source code |
| read.SpatialRNA | Man page Source code |
| read.VisiumSpatialRNA | Man page |
| remap_celltypes | Source code |
| replintegrate | Source code |
| replintegrate_batch | Source code |
| replintegrate_shrink_estimates | Source code |
| replintegrate_two_groups | Source code |
| repliterate | Source code |
| restrict_counts | Man page Source code |
| restrict_puck | Man page Source code |
| restrict_reference | Source code |
| restrict_reference_cell_types | Source code |
| run.CSIDE | Man page Source code |
| run.CSIDE.general | Man page Source code |
| run.CSIDE.intercept | Source code |
| run.CSIDE.nonparam | Man page Source code |
| run.CSIDE.regions | Man page Source code |
| run.CSIDE.replicates | Man page Source code |
| run.CSIDE.single | Man page Source code |
| run.RCTD | Man page Source code |
| run.RCTD.replicates | Man page Source code |
| save.CSIDE.replicates | Man page Source code |
| save.Reference | Source code |
| save.SpatialRNA | Source code |
| set_cell_types_assigned | Man page Source code |
| set_global_Q_all | Source code |
| set_likelihood_vars | Man page Source code |
| set_likelihood_vars_sigma | Source code |
| solveIRWLS.effects_trust | Source code |
| solveIRWLS.weights | Source code |
| solveOLS | Source code |
| solveWLS | Source code |
| solve_sq | Source code |
| spacexr | Man page |
| subset_rctd | Source code |
| sweep1t | Source code |
| sweep2t | Source code |
| sweep3t_all | Source code |
| test_genes_sig_post | Source code |
| test_single_beads | Source code |
| write_de_summary | Man page Source code |
