Man pages for saeyslab/multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
| add_empirical_pval_fdr | Add empirical p-values and adjusted p-values to the DE output... |
| add_extra_criterion | add_extra_criterion |
| alias_to_symbol_SCE | Convert aliases to official gene symbols in a... |
| combine_sender_receiver_de | combine_sender_receiver_de |
| combine_sender_receiver_info_ic | combine_sender_receiver_info_ic |
| compare_normal_emp_pvals | compare_normal_emp_pvals |
| fix_frq_df | fix_frq_df |
| geneinfo_alias_human | Gene annotation information: version 2 - january 2022 -... |
| geneinfo_alias_mouse | Gene annotation information: version 2 - january 2022 -... |
| generate_prioritization_tables | generate_prioritization_tables |
| generate_prioritization_tables_condition_specific_celltypes_receiver | generate_prioritization_tables_condition_specific_celltypes_receiver |
| generate_prioritization_tables_condition_specific_celltypes_sender | generate_prioritization_tables_condition_specific_celltypes_sender |
| generate_prioritization_tables_sampleAgnostic_multifactorial | generate_prioritization_tables_sampleAgnostic_multifactorial |
| get_abundance_info | get_abundance_info |
| get_avg_pb_exprs | get_avg_pb_exprs |
| get_DE_info | get_DE_info |
| get_DE_info_sampleAgnostic | get_DE_info_sampleAgnostic |
| get_empirical_pvals | get_empirical_pvals |
| get_FDR_empirical | Add empirical p-values and adjusted p-values to a subset of... |
| get_FDR_empirical_plots | Get diagnostic plots of the empirical null. |
| get_FDR_empirical_plots_all | Get diagnostic plots of the empirical null. |
| get_frac_exprs | get_frac_exprs |
| get_frac_exprs_sampleAgnostic | get_frac_exprs_sampleAgnostic |
| get_ligand_activities_targets_DEgenes | get_ligand_activities_targets_DEgenes |
| get_ligand_activities_targets_DEgenes_beta | get_ligand_activities_targets_DEgenes_beta |
| get_muscat_exprs_avg | get_muscat_exprs_avg |
| get_muscat_exprs_frac | get_muscat_exprs_frac |
| get_pseudobulk_logCPM_exprs | get_pseudobulk_logCPM_exprs |
| get_top_n_lr_pairs | get_top_n_lr_pairs |
| infer_intercellular_regulatory_network | infer_intercellular_regulatory_network |
| ligand_target_matrix_test | Ligand-Target Matrix: subset NicheNet 2.0. |
| lr_target_prior_cor_inference | lr_target_prior_cor_inference |
| make_circos_group_comparison | make_circos_group_comparison |
| make_circos_one_group | make_circos_one_group |
| make_DEgene_dotplot_pseudobulk | make_DEgene_dotplot_pseudobulk |
| make_DEgene_dotplot_pseudobulk_batch | make_DEgene_dotplot_pseudobulk_batch |
| make_DEgene_dotplot_pseudobulk_reversed | make_DEgene_dotplot_pseudobulk_reversed |
| make_ggraph_ligand_target_links | make_ggraph_ligand_target_links |
| make_ggraph_signaling_path | make_ggraph_signaling_path |
| make_ligand_activity_plots | make_ligand_activity_plots |
| make_ligand_activity_target_plot | make_ligand_activity_target_plot |
| make_ligand_receptor_violin_plot | make_ligand_receptor_violin_plot |
| make_lite_output | make_lite_output |
| make_lite_output_condition_specific | make_lite_output_condition_specific |
| make_lr_target_correlation_plot | make_lr_target_correlation_plot |
| make_lr_target_prior_cor_heatmap | make_lr_target_prior_cor_heatmap |
| make_lr_target_scatter_plot | make_lr_target_scatter_plot |
| makenames_SCE | make.names of all genes in a SingleCellExperiment Object |
| make_sample_lr_prod_activity_batch_plots | make_sample_lr_prod_activity_batch_plots |
| make_sample_lr_prod_activity_plots | make_sample_lr_prod_activity_plots |
| make_sample_lr_prod_activity_plots_Omnipath | make_sample_lr_prod_activity_plots_Omnipath |
| make_sample_lr_prod_plots | make_sample_lr_prod_plots |
| make_target_violin_plot | make_target_violin_plot |
| multi_nichenet_analysis | multi_nichenet_analysis |
| multi_nichenet_analysis_sampleAgnostic | multi_nichenet_analysis_sampleAgnostic |
| p.adjust_empirical | Get empirical p-values and adjusted p-values. |
| perform_muscat_de_analysis | perform_muscat_de_analysis |
| prioritize_condition_specific_receiver | prioritize_condition_specific_receiver |
| prioritize_condition_specific_sender | prioritize_condition_specific_sender |
| process_abundance_expression_info | process_abundance_expression_info |
| process_abund_info | process_abund_info |
| process_geneset_data | process_geneset_data |
| process_info_to_ic | process_info_to_ic |
| sce | SingleCellExperiment object containing scRNAseq data... |
| visualize_network | visualize_network |
