# Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics

## Documentation for package ‘BulkSignalR’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F G I L M N O P R S T U misc

## -- A --

addClusterComp | Add a comparison between two clusters of samples
addClusterComp-method | 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

## -- B --

bodyMap.mouse | Mouse transcriptoms across tissues
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
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
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
bubblePlotPathwaysLR | Bubble Plot to explore LR & Pathways

## -- C --

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
coerce-method | Convert BSRDataModel to BSRDataModelComp
colClusterA | Cluster A columns accessor
colClusterA-method | Cluster A columns accessor
colClusterB | Cluster B columns accessor
colClusterB-method | Cluster B columns accessor
comparison | Comparisons list accessor
comparison-method | Comparisons list accessor
comparisonName | Comparison name accessor
comparisonName-method | Comparison name accessor
convertToHuman | Transpose to Human Gene Names
createResources | Create all resources

## -- D --

differentialStats | Cluster comparison statistics accessor
differentialStats-method | Cluster comparison statistics accessor

## -- F --

findOrthoGenes | Orthologs Gene Names

## -- G --

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
getPathwayStats-method | Basic statistics about hit pathways
getResource | Get resources from the cache

## -- I --

immune.signatures | Immune cell gene signatures
inferenceParameters | Inference parameters accessor
inferenceParameters-method | Inference parameters accessor
initialOrganism | organism accessor
initialOrganism-method | organism accessor
initialOrthologs | Model parameter accessor
initialOrthologs-method | Model parameter accessor

## -- L --

learnParameters | Training of BulkSignalR model parameters
learnParameters-method | Training of BulkSignalR model parameters
ligands | ligands accessor
ligands-method | ligands accessor
logTransformed | log.transformed accessor
logTransformed-method | log.transformed accessor
LRinter | LRinter accessor
LRinter-method | LRinter accessor
LRinterScore | Simplified LRinter accessor with focus on the LR-score
LRinterScore-method | Simplified LRinter accessor with focus on the LR-score
LRinterShort | Simplified LRinter accessor reporting the essential columns
LRinterShort-method | Simplified LRinter accessor reporting the essential columns

## -- M --

maxLigandSpatialCounts | Get maximal ligand expression at nearby locations
mu | Mu accessor
mu-method | Mu accessor

## -- N --

ncounts | Normalized count matrix accessor
ncounts-method | Normalized count matrix accessor
normalization | Normalization accessor
normalization-method | Normalization accessor

## -- O --

ortholog.dict | A skinny data frame used in the mouse workflow

## -- P --

p.EMT | Partial EMT gene signature
parameters | Model parameter accessor
parameters-method | Model parameter accessor
pathways | pathways accessor
pathways-method | pathways accessor

## -- R --

receptors | receptors accessor
receptors-method | receptors accessor
reduceToBestPathway | Keep one pathway per ligand-receptor pair
reduceToBestPathway-method | Keep one pathway per ligand-receptor pair
reduceToLigand | Aggregate the receptors of a same ligand
reduceToLigand-method | Aggregate the receptors of a same ligand
reduceToPathway | Aggregate ligands and receptors at the pathway level
reduceToPathway-method | Aggregate ligands and receptors at the pathway level
reduceToReceptor | Aggregate the ligands of a same receptor
reduceToReceptor-method | Aggregate the ligands of a same receptor
relateToGeneSet | Relate ligands to a gene set
removeClusterComp | Remove a comparison from a BSRDataModelComp object.
removeClusterComp-method | Remove a comparison from a BSRDataModelComp object.
rescoreInference | Inference re-scoring
rescoreInference-method | 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
resetToInitialOrganism-method | Reset gene names to initial organism provided in the first instance

## -- S --

scoreLRGeneSignatures | Score ligand-receptor gene signatures
scoreLRGeneSignatures-method | 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
sourceComparisonName-method | 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

## -- T --

tgCorr | Target gene correlations accessor
tgCorr-method | Target gene correlations accessor
tgExpr | Target gene expression accessor
tgExpr-method | Target gene expression accessor
tgGenes | Target genes accessor
tgGenes-method | Target genes accessor
tgLogFC | Target gene logFC accessor
tgLogFC-method | Target gene logFC accessor
tgPval | Target gene P-values accessor
tgPval-method | Target gene P-values accessor
tme.signatures | Tumor microenvironment gene signatures

## -- U --

updateInference | Inference updating
updateInference-method | Inference updating

## -- misc --

.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