annotateGO              Perform GO annotation of input data
annotatePathways        Annotate pathways for input data
buildPairsbyFunctionMatrix
                        Build binary matrix with int-pairs in rows,
                        functions in cols
checkLL_RR              Manually change the annotation of L-L and R-R
                        pairs
circlePlot              Plot circle plot
combineAnnotations      Combine GO annotation and pathways in a unique
                        object
createBarPlot1_ggplot   Create ggplot barplot to be saved in tiff
createBarPlot2_CV       Create barplot of number of interaction for
                        selected cluster
createBarPlot2_ggplot   Create ggplot barplot of Nint per cluster
                        selected
createBarPlot_CV        Create Barplot cluster-verse
createNetwork           Create Network of clusters
dendroIntPairModules    Get dendrogram of int pair modules
elbowPoint              Determine the elbow point on a curve (from
                        package akmedoids)
ensemblLink             Get html link to ensembl
getBack2BackBarplot     Get back-to-back barplot for 2 conditions
                        comparison
getBarplotDF            Get dataframe for plotting barplot (all
                        clusters)
getBarplotDF2           Get dataframe for barplot (by cluster)
getClusterNames         Get clusters names from initial input data
getClusterNetwork       Creating edges dataframe for network of
                        clusters
getClusterSize          Get Clusters size
getDotPlot_selInt       Functions to plot DotPlots
getGObiomaRt            Connection to Ensembl via biomaRt to get GO
                        terms
getGeneTable            Get table for gene-verse
getHitsf                Subfunction to calculate significant functions
                        by permutation test
getIntFlow              Get subset of interactions corresponding to a
                        certain viewpoint and flow
getNtermsBYdb           Calculate number of terms of a database
getNumLR                Get number of unique ligands and receptors
getRadarPlot            Get radar plot of relative numbers of
                        interactions for a certain cell type
getRankedTerms          Get table with ranked functional terms
getSignificantFunctions
                        Calculate significant function per intpair
                        module
getSunburst             Get Sunburst plot of selected functional terms
getUMAPipModules        Get UMAP for IP modules
getUniqueDotplot        Plot dotplot containing only unique
                        int-pair/cluster pairs with many conditions
goLink                  Get GO link
input.data              Input Data example
read.CPDBv2             Read output from CellPhoneDB v2.
read.SCsignalR          Read output from SingleCellSignalR
read.customInput        Read custom input file and re-structure it with
                        InterCellar format
run_app                 Run the Shiny Application
subsetFuncMatBYFlow     Subset pairs-function matrix by selected flow
swap.RLint              Swaps interaction pairs that are R-L to L-R
uniprotLink             Get html link to uniprot
updateInputLR           Function that orders all interaction pairs as
                        L-R. Leaves unchanged the R-R and L-L
