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:
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
- 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
Last updated from:8f0a5748b8 (on main). Checks:5 WARNING, 2 OK, 2 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | WARNING | 899 | ||
| source / vignettes | OK | 436 | ||
| linux-release-x86_64 | WARNING | 813 | ||
| macos-release-arm64 | WARNING | 566 | ||
| macos-oldrel-arm64 | FAIL | 110 | ||
| windows-devel | WARNING | 544 | ||
| windows-release | WARNING | 775 | ||
| windows-oldrel | FAIL | 836 | ||
| wasm-release | OK | 312 |
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
Last update: 2026-01-23
Started: 2026-01-23
Last update: 2026-01-23
Started: 2026-01-23
Last update: 2026-01-23
Started: 2026-01-23
