Man pages for saezlab/ligrec_decoupler
LIANA: a LIgand-receptor ANalysis frAmework
| assign_ligrecs | Helper function to obtain distinct transmitter and receiver... |
| assign_lr_weights | Helper function to assign weights |
| calculate_gini | Function to calculate gini coefficients for source and target... |
| call_cellchat | Run CellChat with OmniPath function [[DEPRECATED]] |
| call_connectome | Function to call connectome with databases from OmniPath... |
| call_italk | Run iTALK with OmniPath data [[DEPRECATED]] |
| call_natmi | Call NATMI Pipeline from R with Resources Querried from... |
| call_sca | Function to call SingleCellSignalR with databases from... |
| call_squidpy | Call Squidpy Pipeline via reticulate with OmniPath and format... |
| cellchat_formatDB | Helper Function to Format CellChatDB |
| cellphonedb_score | Function to calculate p-values as in CellPhoneDB |
| check_if_dissociated | Helper Function to check if there are dissociated entities... |
| chord_freq | Frequency ChordDiagram |
| compile_ligrec | Function to get unfiltered intercell resources For each... |
| compute_mi_dist | Compute mutual information distance from expression vectors |
| compute_nst_from_matrix | Compute non-self talk scores from matrix |
| compute_nst_scores | Compute non-self talk scores from SingleCellExperiment object |
| compute_pem_scores | Compute Preferential Expression Measure scores from... |
| conn_formatDB | Helper Function to convert Omni to Connectome resource Format |
| cytotalk_score | Compute cross-talk score from a Seurat Object (DEPRECATED) |
| decomplexify | Helper Function to 'decomplexify' ligands and receptors into... |
| decompose_tensor | Wrapper function to run 'cell2cell_tensor' decomposition on a... |
| dot-antilog1m | Helper function to inverse logged counts |
| dot-rank_matrix | Function to convert a list of characters to a ranked matrix... |
| dot-sp_costrain | Weigh by spatial constrans |
| filter_nonabundant_celltypes | Filter nun-abundant cell types |
| FormatConnectome | Helper function to filter and format connectome |
| FormatiTALK | Helper Function to Filter and format iTalk results |
| FormatNatmi | Load NATMI results from folder and format appropriately |
| FormatSCA | Helper function to format SingleCellSignalR results |
| generate_homologs | Function to generate a homologous OmniPath resource |
| generate_lr_geneset | Generate a geneset resource for each LR |
| generate_orthologs | Deprecated call to generate_homologs |
| genesymbol_to_uniprot | Helper Function to translate to UniProt |
| get_abundance_summary | Function to get abundance summary |
| get_c2c_factors | Returns tensor cell2cell results |
| get_cellcall | Function to Obtain the CellCall database |
| get_cellchat_missing | Helper Function to get Missing Interactions from OG... |
| get_connectome | Function to obtain connectome-like weights |
| get_curated_omni | Function to Generate the Curated (Default) LIANA resource |
| get_homologene_dict | Helper function to get homologene dictionary |
| get_logfc | Function to obtain logFC weights |
| get_lr_resources | Helper function that returns the name of each intercell... |
| get_natmi | Function to obtain NATMI-like weights |
| get_partners | Retrieves intercellular communication partners (ligands or... |
| get_permutations | Helper Function to generate shuffled means |
| get_sca | Function to obtain SingleCellSignalR-like scores |
| get_up_dict | Helper function to get UniProt dictionary |
| heat_freq | Communication Frequency heatmap plot |
| join_means | Join Expression per Cluster |
| liana_aggregate | Function to Aggregate CCC Method Results |
| liana_bysample | Wrapper around 'liana_wrap' to run liana for each sample. |
| liana_call | Wrapper Function to obtain scores via liana_pipe |
| liana_defaults | Function to pass Default Arguments for each method |
| liana_dotplot | Liana dotplot interactions by source and target cells |
| liana_heatmap | Communication by cell type Heatmap |
| liana_message | LIANA message/warning helper function to allow for verbosity |
| liana_pipe | Liana Pipe which runs DE analysis and merges needed... |
| liana_prep | Function to handle different types of object as input and do... |
| liana_scores | Function to obtain different scoring schemes |
| liana_tensor_c2c | Wrapper function to run 'cell2cell_tensor' with LIANA output. |
| liana_wrap | LIANA wrapper function |
| map_custom | Helper custom map function |
| mean0 | Helper Function which returns the mean, unless there is a 0... |
| mean_permute | Function to calculate mean LR expression from shuffled... |
| min0 | Helper Function which returns the value closest to 0 |
| minmax | Helper min-max function |
| omnipath_partners | Retrieves intercellular communication partners (transmitters... |
| plot_abundance_summary | Function to Plot Abundance Summary |
| plot_c2c_cells | Plot the product of loadings between the source and target... |
| plot_c2c_overview | Function to plot an Overview of tensor-c2c results |
| plot_context_boxplot | Generate boxplots with significance |
| plot_context_heat | Plot a Heatmap of context loadings |
| plot_lr_heatmap | Function to plot a UMAP of context loadings |
| preprocess_scores | Helper function to deal with tensor sparsity and liana's... |
| rank_aggregate | Aggregate CCC Method results and by both magnitude and... |
| rank_method | Helper function to rank each method |
| recode.character2 | Modified 'dplyr::recode' function |
| recomplexify | Helper function to account for complexes in the resources |
| sca_formatDB | Helper Function to convert Omni to LRdb Format |
| ScoreSpecifics-class | S4 Class used to generate aggregate/consesus scores for the... |
| select_resource | Helper Function to Handle resource choices |
| show_homologene | Helper function to show available organisms via OmnipathR's... |
| show_methods | Helper Function to return the methods in LIANA |
| show_resources | Helper Function to return the Resources in LIANA |
