.formatPathwaysFromGmt
                        Transform gmt file to data frame
.formatPathwaysFromJson
                        Format a data frame according to json input
.formatPathwaysFromTxt
                        Read dataframe from txt file
.testCacheFiles         Check there is a well formatted cache
.testRemoteServer       Check whether the reference DB server is up
BSRClusterComp          Definition of the comparison between two
                        clusters of samples
BSRClusterComp-class    BulkSignalR Cluster Comparison Object
BSRDataModel            Constructor of the BSRDataModel class
BSRDataModel-class      BulkSignalR Data Model Object
BSRDataModelComp        Constructor of the BSRDataModelComp class
BSRDataModelComp-class
                        BulkSignalR Data Model Compare Object
BSRInference            Inference of ligand-receptor interactions
BSRInference-class      BulkSignalR Inference Object
BSRInferenceComp        Inference of ligand-receptor interactions based
                        on regulation
BSRInferenceComp-class
                        BulkSignalR cluster comparison-based inference
                        object
BSRSignature            Extract gene signatures of LR pair activity
BSRSignature-class      BulkSignalR ligand-receptor signature Object
BSRSignatureComp        Extract gene signatures of LR pair activity
BSRSignatureComp-class
                        BulkSignalR ligand-receptor signature object
                        for cluster comparisons
LRinter                 LRinter accessor
LRinterScore            Simplified LRinter accessor with focus on the
                        LR-score
LRinterShort            Simplified LRinter accessor reporting the
                        essential columns
addClusterComp          Add a comparison between two clusters of
                        samples
alluvialPlot            Alluvial plot
annotation.spa          A skinny data frame used in the spatial
                        workflow
assignCellTypesToInteractions
                        Assign cell types to L-R interactions
bodyMap.mouse           Mouse transcriptoms across tissues
bsrdm                   A skinny BSRDataModel object related to sdc.
bsrdm.comp              A skinny BSRDataModelComp object related to
                        sdc.
bsrdm.spa               A skinny BSRDataModel object related to a
                        spatial data set
bsrinf                  A skinny BSRInference object related to sdc.
bsrinf.comp             A skinny BSRInferenceComp object related to
                        sdc.
bsrinf.mouse            A skinny BSRInference object related to
                        bodyMap.mouse
bsrinf.spa              A skinny BSR-inference object related to
                        spatial data set
bubblePlotPathwaysLR    Bubble Plot to explore LR & Pathways
cacheClear              Delete cache content.
cacheInfo               Get cache content information.
cacheVersion            Check whether remote resource files have been
                        changed.
cellTypeFrequency       Cell type frequencies in relations to gene sets
cellularNetwork         Build a cellular network
cellularNetworkTable    Build a table describing a cellular network
chordDiagramLR          Chord Diagram of LR interactions with
                        correlations
coerce                  Convert BSRDataModel to BSRDataModelComp
colClusterA             Cluster A columns accessor
colClusterB             Cluster B columns accessor
comparison              Comparisons list accessor
comparisonName          Comparison name accessor
convertToHuman          Transpose to Human Gene Names
createResources         Create all resources
differentialStats       Cluster comparison statistics accessor
findOrthoGenes          Orthologs Gene Names
generateSpatialPlots    Generate L-R interaction score spatial plots in
                        a folder
getLRIntracellNetwork   Generate a ligand-receptor-downstream signaling
                        network
getLRNetwork            Generate a ligand-receptor network
getPathwayStats         Basic statistics about hit pathways
getResource             Get resources from the cache
immune.signatures       Immune cell gene signatures
inferenceParameters     Inference parameters accessor
initialOrganism         organism accessor
initialOrthologs        Model parameter accessor
learnParameters         Training of BulkSignalR model parameters
ligands                 ligands accessor
logTransformed          log.transformed accessor
maxLigandSpatialCounts
                        Get maximal ligand expression at nearby
                        locations
mu                      Mu accessor
ncounts                 Normalized count matrix accessor
normalization           Normalization accessor
ortholog.dict           A skinny data frame used in the mouse workflow
p.EMT                   Partial EMT gene signature
parameters              Model parameter accessor
pathways                pathways accessor
receptors               receptors accessor
reduceToBestPathway     Keep one pathway per ligand-receptor pair
reduceToLigand          Aggregate the receptors of a same ligand
reduceToPathway         Aggregate ligands and receptors at the pathway
                        level
reduceToReceptor        Aggregate the ligands of a same receptor
relateToGeneSet         Relate ligands to a gene set
removeClusterComp       Remove a comparison from a BSRDataModelComp
                        object.
rescoreInference        Inference re-scoring
resetLRdb               Modify LRdb database
resetNetwork            Import a refernce network of your own
resetPathways           Import pathways from a file or data frame
resetToInitialOrganism
                        Reset gene names to initial organism provided
                        in the first instance
scoreLRGeneSignatures   Score ligand-receptor gene signatures
scoreSignatures         Generic gene signature scoring
sdc                     Salivary duct carcinoma transcriptoms
separatedLRPlot         Generate separated plots for a L-R interaction
signatureHeatmaps       Heatmap function to dissect one pathway
                        signature
simpleHeatmap           Heatmap function for LR scores
smoothSpatialCounts     Smooth spatial expression data
sourceComparisonName    Source comparison name accessor
spatialAssociation      Statistical association of scores with area
                        labels
spatialAssociationPlot
                        Heatmap plot of association of scores with area
                        labels
spatialDiversityPlot    2D-projection of spatial score distributions
spatialIndexPlot        Generate a visual index of spatial score
                        distributions
spatialPlot             L-R interaction score spatial display
summarizedCellularNetwork
                        Build a summary cellular network
tgCorr                  Target gene correlations accessor
tgExpr                  Target gene expression accessor
tgGenes                 Target genes accessor
tgLogFC                 Target gene logFC accessor
tgPval                  Target gene P-values accessor
tme.signatures          Tumor microenvironment gene signatures
updateInference         Inference updating
