Files in saeyslab/multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
.DS_Store
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R-raw/add_data.R
R/condition_specific_celltypes.R
R/data.R
R/expression_processing.R
R/functions_OLINK.R
R/ligand_activities.R
R/lr_target_correlation.R
R/muscat_de.R
R/pipeline.R
R/pipeline_wrappers.R
R/plotting.R
R/prioritization.R
README.Rmd
README.md
data/geneinfo_alias_human.rda
data/geneinfo_alias_mouse.rda
data/ligand_target_matrix_test.rda
data/sce.rda
inst/CITATION
man/add_empirical_pval_fdr.Rd
man/add_extra_criterion.Rd
man/alias_to_symbol_SCE.Rd
man/combine_sender_receiver_de.Rd
man/combine_sender_receiver_info_ic.Rd
man/compare_normal_emp_pvals.Rd
man/fix_frq_df.Rd
man/geneinfo_alias_human.Rd
man/geneinfo_alias_mouse.Rd
man/generate_prioritization_tables.Rd
man/generate_prioritization_tables_condition_specific_celltypes_receiver.Rd
man/generate_prioritization_tables_condition_specific_celltypes_sender.Rd
man/generate_prioritization_tables_sampleAgnostic_multifactorial.Rd
man/get_DE_info.Rd
man/get_DE_info_sampleAgnostic.Rd
man/get_FDR_empirical.Rd
man/get_FDR_empirical_plots.Rd
man/get_FDR_empirical_plots_all.Rd
man/get_abundance_info.Rd
man/get_avg_pb_exprs.Rd
man/get_empirical_pvals.Rd
man/get_frac_exprs.Rd
man/get_frac_exprs_sampleAgnostic.Rd
man/get_ligand_activities_targets_DEgenes.Rd
man/get_ligand_activities_targets_DEgenes_beta.Rd
man/get_muscat_exprs_avg.Rd
man/get_muscat_exprs_frac.Rd
man/get_pseudobulk_logCPM_exprs.Rd
man/get_top_n_lr_pairs.Rd
man/infer_intercellular_regulatory_network.Rd
man/ligand_target_matrix_test.Rd
man/lr_target_prior_cor_inference.Rd
man/make_DEgene_dotplot_pseudobulk.Rd
man/make_DEgene_dotplot_pseudobulk_batch.Rd
man/make_DEgene_dotplot_pseudobulk_reversed.Rd
man/make_circos_group_comparison.Rd
man/make_circos_one_group.Rd
man/make_ggraph_ligand_target_links.Rd
man/make_ggraph_signaling_path.Rd
man/make_ligand_activity_plots.Rd
man/make_ligand_activity_target_plot.Rd
man/make_ligand_receptor_violin_plot.Rd
man/make_lite_output.Rd
man/make_lite_output_condition_specific.Rd
man/make_lr_target_correlation_plot.Rd
man/make_lr_target_prior_cor_heatmap.Rd
man/make_lr_target_scatter_plot.Rd
man/make_sample_lr_prod_activity_batch_plots.Rd
man/make_sample_lr_prod_activity_plots.Rd
man/make_sample_lr_prod_activity_plots_Omnipath.Rd
man/make_sample_lr_prod_plots.Rd
man/make_target_violin_plot.Rd
man/makenames_SCE.Rd
man/multi_nichenet_analysis.Rd
man/multi_nichenet_analysis_sampleAgnostic.Rd
man/p.adjust_empirical.Rd
man/perform_muscat_de_analysis.Rd
man/prioritize_condition_specific_receiver.Rd
man/prioritize_condition_specific_sender.Rd
man/process_abund_info.Rd
man/process_abundance_expression_info.Rd
man/process_geneset_data.Rd
man/process_info_to_ic.Rd
man/sce.Rd
man/visualize_network.Rd
multinichenetr.Rproj
output_interpretation.pdf
parameter_interpretation.pdf
tests/test_pipeline.R
tests/testthat/Rplots.pdf
tests/testthat/test-pipeline.R
vignettes/.DS_Store
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