Package index • multinichenetr

Main Pipeline

Core analysis functions

multi_nichenet_analysis(): multi_nichenet_analysis

multi_nichenet_analysis_sampleAgnostic(): multi_nichenet_analysis_sampleAgnostic

make_lite_output(): make_lite_output

make_lite_output_condition_specific(): make_lite_output_condition_specific

Expression Processing

Functions for processing expression data

get_frac_exprs(): get_frac_exprs

get_frac_exprs_sampleAgnostic(): get_frac_exprs_sampleAgnostic

get_muscat_exprs_avg(): get_muscat_exprs_avg

get_muscat_exprs_frac(): get_muscat_exprs_frac

get_avg_pb_exprs(): get_avg_pb_exprs

get_pseudobulk_logCPM_exprs(): get_pseudobulk_logCPM_exprs

get_abundance_info(): get_abundance_info

process_abundance_expression_info(): process_abundance_expression_info

Differential Expression

DE analysis functions

get_DE_info(): get_DE_info

get_DE_info_sampleAgnostic(): get_DE_info_sampleAgnostic

perform_muscat_de_analysis(): perform_muscat_de_analysis

p.adjust_empirical(): Get empirical p-values and adjusted p-values.

get_empirical_pvals(): get_empirical_pvals

get_FDR_empirical(): Add empirical p-values and adjusted p-values to a subset of the DE output table.

add_empirical_pval_fdr(): Add empirical p-values and adjusted p-values to the DE output table.

Ligand Activity

NicheNet ligand activity inference

get_ligand_activities_targets_DEgenes(): get_ligand_activities_targets_DEgenes

get_ligand_activities_targets_DEgenes_beta(): get_ligand_activities_targets_DEgenes_beta

infer_intercellular_regulatory_network(): infer_intercellular_regulatory_network

lr_target_prior_cor_inference(): lr_target_prior_cor_inference

Prioritization

Multi-criteria prioritization functions

generate_prioritization_tables(): generate_prioritization_tables

generate_prioritization_tables_sampleAgnostic_multifactorial(): generate_prioritization_tables_sampleAgnostic_multifactorial

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

prioritize_condition_specific_receiver(): prioritize_condition_specific_receiver

prioritize_condition_specific_sender(): prioritize_condition_specific_sender

add_extra_criterion(): add_extra_criterion

get_top_n_lr_pairs(): get_top_n_lr_pairs

Visualization

Plotting functions

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_circos_group_comparison(): make_circos_group_comparison

make_circos_one_group(): make_circos_one_group

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

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

visualize_network(): visualize_network

get_FDR_empirical_plots(): Get diagnostic plots of the empirical null.

get_FDR_empirical_plots_all(): Get diagnostic plots of the empirical null.

Data Processing Utilities

Helper functions for data manipulation

alias_to_symbol_SCE(): Convert aliases to official gene symbols in a SingleCellExperiment Object

makenames_SCE(): make.names of all genes in a SingleCellExperiment Object

process_abund_info(): process_abund_info

process_info_to_ic(): process_info_to_ic

process_geneset_data(): process_geneset_data

combine_sender_receiver_de(): combine_sender_receiver_de

combine_sender_receiver_info_ic(): combine_sender_receiver_info_ic

fix_frq_df(): fix_frq_df

compare_normal_emp_pvals(): compare_normal_emp_pvals

Example Data

Built-in datasets

sce: SingleCellExperiment object containing scRNAseq data (subsampled)

ligand_target_matrix_test: Ligand-Target Matrix: subset NicheNet 2.0.

geneinfo_alias_human: Gene annotation information: version 2 - january 2022 - suited for alias conversion

geneinfo_alias_mouse: Gene annotation information: version 2 - january 2022 - suited for alias conversion