Package: multinichenetr 2.1.0

multinichenetr: MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

This package allows you the investigate differences in intercellular communication between multiple conditions of interest. It is a flexible framework that enables multi-criteria prioritization of cell-cell communication patterns from scRNAseq datasets with complex experimental designs. These datasets can contain multiple samples (e.g. patients) over different groups of interest (e.g. disease subtypes). With MultiNicheNet, you can now better analyze the differences in cell-cell signaling between the different groups of interest.

Authors:Zaoqu Liu [aut, cre]

multinichenetr_2.1.0.tar.gz
multinichenetr_2.1.0.zip(r-4.7)multinichenetr_2.1.0.zip(r-4.6)multinichenetr_2.1.0.zip(r-4.5)
multinichenetr_2.1.0.tgz(r-4.6-any)multinichenetr_2.1.0.tgz(r-4.5-any)
multinichenetr_2.1.0.tar.gz(r-4.7-any)multinichenetr_2.1.0.tar.gz(r-4.6-any)
multinichenetr_2.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
multinichenetr/json (API)

# Install 'multinichenetr' in R:
install.packages('multinichenetr', repos = c('https://zaoqu-liu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zaoqu-liu/multinichenetr/issues

Pkgdown/docs site:https://zaoqu-liu.github.io

Datasets:
  • 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
  • ligand_target_matrix_test - Ligand-Target Matrix: subset NicheNet 2.0.
  • sce - SingleCellExperiment object containing scRNAseq data

On CRAN:

Conda:

4.32 score 140 scripts 61 exports 357 dependencies

Last updated from:8f0a5748b8 (on main). Checks:5 WARNING, 2 OK, 2 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING899
source / vignettesOK436
linux-release-x86_64WARNING813
macos-release-arm64WARNING566
macos-oldrel-arm64FAIL110
windows-develWARNING544
windows-releaseWARNING775
windows-oldrelFAIL836
wasm-releaseOK312

Exports:add_empirical_pval_fdradd_extra_criterionalias_to_symbol_SCEcombine_sender_receiver_decombine_sender_receiver_info_iccompare_normal_emp_pvalsfix_frq_dfgenerate_prioritization_tablesgenerate_prioritization_tables_condition_specific_celltypes_receivergenerate_prioritization_tables_condition_specific_celltypes_sendergenerate_prioritization_tables_sampleAgnostic_multifactorialget_abundance_infoget_avg_pb_exprsget_DE_infoget_DE_info_sampleAgnosticget_empirical_pvalsget_FDR_empiricalget_FDR_empirical_plotsget_FDR_empirical_plots_allget_frac_exprsget_frac_exprs_sampleAgnosticget_ligand_activities_targets_DEgenesget_ligand_activities_targets_DEgenes_betaget_muscat_exprs_avgget_muscat_exprs_fracget_pseudobulk_logCPM_exprsget_top_n_lr_pairsinfer_intercellular_regulatory_networklr_target_prior_cor_inferencemake_circos_group_comparisonmake_circos_one_groupmake_DEgene_dotplot_pseudobulkmake_DEgene_dotplot_pseudobulk_batchmake_DEgene_dotplot_pseudobulk_reversedmake_ggraph_ligand_target_linksmake_ggraph_signaling_pathmake_ligand_activity_plotsmake_ligand_activity_target_plotmake_ligand_receptor_violin_plotmake_lite_outputmake_lite_output_condition_specificmake_lr_target_correlation_plotmake_lr_target_prior_cor_heatmapmake_lr_target_scatter_plotmake_sample_lr_prod_activity_batch_plotsmake_sample_lr_prod_activity_plotsmake_sample_lr_prod_activity_plots_Omnipathmake_sample_lr_prod_plotsmake_target_violin_plotmakenames_SCEmulti_nichenet_analysismulti_nichenet_analysis_sampleAgnosticp.adjust_empiricalperform_muscat_de_analysisprioritize_condition_specific_receiverprioritize_condition_specific_senderprocess_abund_infoprocess_abundance_expression_infoprocess_geneset_dataprocess_info_to_icvisualize_network

Dependencies:abindannotateAnnotationDbiaodaskpassassortheadbackportsbase64encBBmiscbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64bitopsblmeblobblusterbootbroombslibcachemcallrcarcarDatacaretcaToolscellrangercheckmatecirclizeclassclicliprclockclueclustercodetoolscolorspacecommonmarkComplexHeatmapconflictedcorpcorcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdendextendDerivdiagramDiagrammeRDiceKrigingdigestdoBydoParalleldotCall64dplyrdqrngDTdtplyre1071edgeRellipseemmeansemoaEnvStatsestimabilityevaluatefactoextraFactoMineRfANCOVAfarverfastDummiesfastmapfastmatchfdrtoolfitdistrplusflashClustFNNfontawesomefontBitstreamVerafontLiberationfontquiverforcatsforeachforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsfuturefuture.applygarglegdtoolsgenefiltergenericsGenomicRangesGetoptLongggbeeswarmggforceggiraphggnewscaleggplot2ggpubrggraphggrepelggridgesggsciggsignifggtextglmmTMBGlobalOptionsglobalsgluegoftestgoogledrivegooglesheets4gowergplotsgraphlayoutsgridExtragridtextgtablegtoolshardhathavenherehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttricaidsigraphipredIRangesirlbaisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelavalazyevalleapslhslifecyclelimmalistenvlitedownlme4lmerTestlmtestlocfdrlocfitlubridatemagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemetapodmgcvmimeminiUIminqamlrmlrMBOModelMetricsmodelrmultcompViewmuscatmvtnormnichenetrnlmenloptrnnetnortestnumDerivopensslotelparallellyparallelMapParamHelperspatchworkpbapplypbkrtestpheatmappillarpkgconfigplotlyplyrpngpolyclippolynomprettyunitspROCprocessxprodlimprogressprogressrpromisesproxypspurrrquantregR6raggrandomForestRANNrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLRdpackreadrreadxlrecipesreformulasremaCorrematchrematch2reprexreshape2reticulateRhpcBLASctlrjsonrlangrmarkdownROCRrpartrprojrootRSpectraRSQLiterstatixrstudioapirsvdRtsnervestS4ArraysS4VectorsS7sandwichsassScaledMatrixscalesscaterscattermorescatterplot3dscransctransformscuttleselectrSeqinfoSeuratSeuratObjectshadowtextshapeshinyshowtextshowtextdbSingleCellExperimentsitmosmoofsnowsourcetoolsspspamSparseArraySparseMsparsevctrsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsvasyssysfontssystemfontstensortextshapingtibbletidygraphtidyrtidyselecttidyversetimechangetimeDatetinytexTMBtweenrtzdbUpSetRurcautf8uuiduwotvariancePartitionvctrsviporviridisviridisLitevisNetworkvroomwithrxfunXMLxml2xtableXVectoryamlzoo

Algorithm & Methodology
Overview | Theoretical Framework | The Cell-Cell Communication Inference Problem | Why Multi-Sample Analysis? | Core Algorithms | 1. Pseudobulk Aggregation | 2. Differential Expression Analysis | 3. NicheNet Ligand Activity Inference | 4. Multi-Criteria Prioritization | Biological Scenarios | Mathematical Details | Expression Fraction Calculation | Cell-Type Specificity Score | Prioritization Score Aggregation | Comparison with Other Methods | Performance Considerations | Computational Complexity | Parallelization | References

Last update: 2026-01-23
Started: 2026-01-23

Quick Start Guide
Introduction | Key Features | Installation | From R-Universe (Recommended) | From GitHub | Quick Start Example | Load Required Packages | Load Example Data | Define Analysis Parameters | Load Prior Knowledge Networks | Run MultiNicheNet Analysis | Explore Results | Basic Visualization | Output Structure | Next Steps | Session Info | Citation

Last update: 2026-01-23
Started: 2026-01-23

Visualization Gallery
Introduction | Overview of Visualization Functions | Sample-Level Visualizations | Ligand-Receptor Product Plots | Differential Expression Visualization | Network Visualizations | Circos Plots | Chord Diagrams | Multi-Criteria Bubble Plots | Mushroom Plots | Ligand Activity Visualizations | Activity Heatmaps | Target Gene Visualizations | Target Gene Expression | Summary Statistics | Overview Barplots | Customization Tips | Color Palettes | Export High-Quality Figures | Session Information

Last update: 2026-01-23
Started: 2026-01-23

Readme and manuals

Help Manual

Help pageTopics
Add empirical p-values and adjusted p-values to the DE output table.add_empirical_pval_fdr
add_extra_criterionadd_extra_criterion
Convert aliases to official gene symbols in a SingleCellExperiment Objectalias_to_symbol_SCE
combine_sender_receiver_decombine_sender_receiver_de
combine_sender_receiver_info_iccombine_sender_receiver_info_ic
compare_normal_emp_pvalscompare_normal_emp_pvals
fix_frq_dffix_frq_df
Gene annotation information: version 2 - january 2022 - suited for alias conversiongeneinfo_alias_human
Gene annotation information: version 2 - january 2022 - suited for alias conversiongeneinfo_alias_mouse
generate_prioritization_tablesgenerate_prioritization_tables
generate_prioritization_tables_condition_specific_celltypes_receivergenerate_prioritization_tables_condition_specific_celltypes_receiver
generate_prioritization_tables_condition_specific_celltypes_sendergenerate_prioritization_tables_condition_specific_celltypes_sender
generate_prioritization_tables_sampleAgnostic_multifactorialgenerate_prioritization_tables_sampleAgnostic_multifactorial
get_abundance_infoget_abundance_info
get_avg_pb_exprsget_avg_pb_exprs
get_DE_infoget_DE_info
get_DE_info_sampleAgnosticget_DE_info_sampleAgnostic
get_empirical_pvalsget_empirical_pvals
Add empirical p-values and adjusted p-values to a subset of the DE output table.get_FDR_empirical
Get diagnostic plots of the empirical null.get_FDR_empirical_plots
Get diagnostic plots of the empirical null.get_FDR_empirical_plots_all
get_frac_exprsget_frac_exprs
get_frac_exprs_sampleAgnosticget_frac_exprs_sampleAgnostic
get_ligand_activities_targets_DEgenesget_ligand_activities_targets_DEgenes
get_ligand_activities_targets_DEgenes_betaget_ligand_activities_targets_DEgenes_beta
get_muscat_exprs_avgget_muscat_exprs_avg
get_muscat_exprs_fracget_muscat_exprs_frac
get_pseudobulk_logCPM_exprsget_pseudobulk_logCPM_exprs
get_top_n_lr_pairsget_top_n_lr_pairs
infer_intercellular_regulatory_networkinfer_intercellular_regulatory_network
Ligand-Target Matrix: subset NicheNet 2.0.ligand_target_matrix_test
lr_target_prior_cor_inferencelr_target_prior_cor_inference
make_circos_group_comparisonmake_circos_group_comparison
make_circos_one_groupmake_circos_one_group
make_DEgene_dotplot_pseudobulkmake_DEgene_dotplot_pseudobulk
make_DEgene_dotplot_pseudobulk_batchmake_DEgene_dotplot_pseudobulk_batch
make_DEgene_dotplot_pseudobulk_reversedmake_DEgene_dotplot_pseudobulk_reversed
make_ggraph_ligand_target_linksmake_ggraph_ligand_target_links
make_ggraph_signaling_pathmake_ggraph_signaling_path
make_ligand_activity_plotsmake_ligand_activity_plots
make_ligand_activity_target_plotmake_ligand_activity_target_plot
make_ligand_receptor_violin_plotmake_ligand_receptor_violin_plot
make_lite_outputmake_lite_output
make_lite_output_condition_specificmake_lite_output_condition_specific
make_lr_target_correlation_plotmake_lr_target_correlation_plot
make_lr_target_prior_cor_heatmapmake_lr_target_prior_cor_heatmap
make_lr_target_scatter_plotmake_lr_target_scatter_plot
make_sample_lr_prod_activity_batch_plotsmake_sample_lr_prod_activity_batch_plots
make_sample_lr_prod_activity_plotsmake_sample_lr_prod_activity_plots
make_sample_lr_prod_activity_plots_Omnipathmake_sample_lr_prod_activity_plots_Omnipath
make_sample_lr_prod_plotsmake_sample_lr_prod_plots
make_target_violin_plotmake_target_violin_plot
make.names of all genes in a SingleCellExperiment Objectmakenames_SCE
multi_nichenet_analysismulti_nichenet_analysis
multi_nichenet_analysis_sampleAgnosticmulti_nichenet_analysis_sampleAgnostic
Get empirical p-values and adjusted p-values.p.adjust_empirical
perform_muscat_de_analysisperform_muscat_de_analysis
prioritize_condition_specific_receiverprioritize_condition_specific_receiver
prioritize_condition_specific_senderprioritize_condition_specific_sender
process_abund_infoprocess_abund_info
process_abundance_expression_infoprocess_abundance_expression_info
process_geneset_dataprocess_geneset_data
process_info_to_icprocess_info_to_ic
SingleCellExperiment object containing scRNAseq data (subsampled)sce
visualize_networkvisualize_network