├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── pkgdown.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── cellchat_pipe.R ├── connectome_pipe.R ├── crosstalk_funs.R ├── get_omnipath.R ├── italk_pipe.R ├── liana_aggregate.R ├── liana_call.R ├── liana_defaults.R ├── liana_ortho.R ├── liana_pipe.R ├── liana_plot.R ├── liana_prep.R ├── liana_recomplexify.R ├── liana_specs.R ├── liana_tensor.R ├── liana_utils.R ├── liana_wrapper.R ├── natmi_pipe.R ├── nonperm_funs.R ├── perm_funs.R ├── sca_pipe.R └── squidpy_pipe.R ├── README.md ├── configure ├── configure.win ├── inst ├── CITATION ├── LRdb.rda ├── example_elbow.csv ├── figures │ └── liana_logo.png ├── human_mouse_orthologues.RDS ├── omni_resources.rds ├── squidpy_pipe.py └── testdata │ ├── input │ ├── converted_seurat.rds │ ├── sce_conv.rds │ ├── seurat_conv.rds │ ├── testdata.rds │ ├── testsce.rds │ └── wrap_sce.rds │ └── output │ ├── cc_res.RDS │ ├── conn_res.RDS │ ├── conn_score.RDS │ ├── conn_score.RDS.orig │ ├── context_df_test.RDS │ ├── decomp.RDS │ ├── italk_res.RDS │ ├── liana_agg_decomplex.RDS │ ├── liana_aggr.RDS │ ├── liana_constrained.RDS │ ├── liana_cpdb.RDS │ ├── liana_cytotalk.RDS │ ├── liana_def_args.RDS │ ├── liana_def_res.RDS │ ├── liana_dotplot_out.RDS │ ├── liana_freq_out.RDS │ ├── liana_house_aggr.RDS │ ├── liana_pipe.RDS │ ├── liana_res.RDS │ ├── liana_res_plus.RDS │ ├── liana_spec_out.RDS │ ├── logfc_score.RDS │ ├── natmi_res.RDS │ ├── natmi_score.RDS │ ├── op_ortho.RDS │ ├── rank_mag_example.RDS │ ├── rank_spec_example.RDS │ ├── recomplex.RDS │ ├── sca_res.RDS │ ├── sca_score.RDS │ └── squidpy_res.RDS ├── liana_env.yml ├── man ├── FormatConnectome.Rd ├── FormatNatmi.Rd ├── FormatSCA.Rd ├── FormatiTALK.Rd ├── ScoreSpecifics-class.Rd ├── assign_ligrecs.Rd ├── assign_lr_weights.Rd ├── calculate_gini.Rd ├── call_cellchat.Rd ├── call_connectome.Rd ├── call_italk.Rd ├── call_natmi.Rd ├── call_sca.Rd ├── call_squidpy.Rd ├── cellchat_formatDB.Rd ├── cellphonedb_score.Rd ├── check_if_dissociated.Rd ├── chord_freq.Rd ├── compile_ligrec.Rd ├── compute_mi_dist.Rd ├── compute_nst_from_matrix.Rd ├── compute_nst_scores.Rd ├── compute_pem_scores.Rd ├── conn_formatDB.Rd ├── cytotalk_score.Rd ├── decomplexify.Rd ├── decompose_tensor.Rd ├── dot-antilog1m.Rd ├── dot-rank_matrix.Rd ├── dot-sp_costrain.Rd ├── filter_nonabundant_celltypes.Rd ├── generate_homologs.Rd ├── generate_lr_geneset.Rd ├── generate_orthologs.Rd ├── genesymbol_to_uniprot.Rd ├── get_abundance_summary.Rd ├── get_c2c_factors.Rd ├── get_cellcall.Rd ├── get_cellchat_missing.Rd ├── get_connectome.Rd ├── get_curated_omni.Rd ├── get_homologene_dict.Rd ├── get_logfc.Rd ├── get_lr_resources.Rd ├── get_natmi.Rd ├── get_partners.Rd ├── get_permutations.Rd ├── get_sca.Rd ├── get_up_dict.Rd ├── heat_freq.Rd ├── join_means.Rd ├── liana_aggregate.Rd ├── liana_bysample.Rd ├── liana_call.Rd ├── liana_defaults.Rd ├── liana_dotplot.Rd ├── liana_heatmap.Rd ├── liana_message.Rd ├── liana_pipe.Rd ├── liana_prep.Rd ├── liana_scores.Rd ├── liana_tensor_c2c.Rd ├── liana_wrap.Rd ├── map_custom.Rd ├── mean0.Rd ├── mean_permute.Rd ├── min0.Rd ├── minmax.Rd ├── omnipath_partners.Rd ├── plot_abundance_summary.Rd ├── plot_c2c_cells.Rd ├── plot_c2c_overview.Rd ├── plot_context_boxplot.Rd ├── plot_context_heat.Rd ├── plot_lr_heatmap.Rd ├── preprocess_scores.Rd ├── rank_aggregate.Rd ├── rank_method.Rd ├── recode.character2.Rd ├── recomplexify.Rd ├── sca_formatDB.Rd ├── select_resource.Rd ├── show_homologene.Rd ├── show_methods.Rd └── show_resources.Rd ├── pkgdown ├── _pkgdown.yml ├── extra.css └── favicon │ ├── android-chrome-192x192.png │ ├── android-chrome-512x512.png │ ├── apple-touch-icon.png │ ├── browserconfig.xml │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ ├── favicon.ico │ ├── favicon.svg │ ├── mstile-150x150.png │ ├── safari-pinned-tab.svg │ └── site.webmanifest ├── tests ├── testthat.R └── testthat │ ├── test-call_cellchat.R │ ├── 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