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

Documentation for package ‘BulkSignalR’ version 1.1.3

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-- 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
createDatabase	Fetch the LR reference database from internet
createResources	Create all resources

-- D --

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

-- F --

Orthologs Gene Names

-- G --

generateSpatialPlots	Generate L-R interaction score spatial plots in a folder
getComplexes	Retrieve LR complexes
getInteractions	Retrieve LR interactions.
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 --

A skinny data frame used in the mouse workflow

-- P --

-- 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