LIANA

liana-wrapper and related functions

liana_aggregate()

Function to Aggregate CCC Method Results

liana_call()

Wrapper Function to obtain scores via liana_pipe

liana_defaults()

Function to pass Default Arguments for each method

liana_pipe()

Liana Pipe which runs DE analysis and merges needed information for LR inference

liana_scores()

Function to obtain different scoring schemes

liana_wrap()

Run LIANA Wrapper

(External) Method calling functions

call_cellchat()

CellChat x Omni Pipe function

call_connectome()

Function to call connectome with databases from OmniPath

call_italk()

Run iTALK with OmniPath data

call_natmi()

Call NATMI Pipeline from R with Resources Querried from OmniPath

call_sca()

Function to call SingleCellSignalR with databases from OmniPath

call_squidpy()

Call Squidpy Pipeline via reticulate with OmniPath and format results

(Internal) Method calling functions

get_connectome()

Function to obtain connectome-like weights

get_logfc()

Function to obtain logFC weights

get_lr_resources()

Helper function that returns the name of each intercell resource in OmniPath

get_natmi()

Function to obtain NATMI-like weights

get_partners()

Retrieves intercellular communication partners (ligands or receptors) from one ligand-receptor resource.

get_sca()

Function to obtain SingleCellSignalR-like scores

Format Method Output

FormatConnectome()

Helper function to filter and format connectome

FormatNatmi()

Load NATMI results from folder and format appropriately

FormatSCA()

Helper function to format SingleCellSignalR results

FormatiTALK()

Helper Function to Filter and format iTalk results

Obtain Default Parametres

Default parametres passed to each method called by liana

liana_defaults()

Function to pass Default Arguments for each method

Show_ or Select_ Functions

Functions used to obtain available methods and resources, lists, etc

show_methods()

Helper Function to return the methods in LIANA

show_resources()

Helper Function to return the Resources in LIANA

select_resource()

Helper Function to Handle resource choices