Package: BulkSignalR 0.99.22

Jean-Philippe Villemin

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

Inference of ligand-receptor (LR) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. BulkSignalR bases its inferences on the LRdb database included in our other package, SingleCellSignalR available from Bioconductor. It relies on a statistical model that is specific to bulk data sets. Different visualization and data summary functions are proposed to help navigating prediction results.

Authors:Jacques Colinge [aut], Jean-Philippe Villemin [cre]

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BulkSignalR.pdf |BulkSignalR.html✨
BulkSignalR/json (API)
NEWS

# Install 'BulkSignalR' in R:
install.packages('BulkSignalR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • annotation.spa - A skinny dataframe used in the spatial workflow
  • bodyMap.mouse - Mouse transcriptomes across tissues
  • bsrdm - A skinny BSR-dataModel object related to sdc.
  • bsrdm.comp - A skinny BSR-dataModelComp object related to sdc.
  • bsrdm.spa - A skinny BSR-dataModel object related to spatial dataset
  • bsrinf - A skinny BSR-Inference object related to sdc.
  • bsrinf.comp - A skinny BSR-InferenceComp object related to sdc.
  • bsrinf.mouse - A skinny BSR-inference object related to bodyMap.mouse
  • bsrinf.spa - A skinny BSR-inference object related to spatial dataset
  • immune.signatures - Immune cell gene signatures
  • ortholog.dict - A skinny dataframe used in the mouse workflow
  • p.EMT - Partial EMT gene signature
  • sdc - Salivary duct carcinoma transcriptomes
  • tme.signatures - Tumor microenvironment gene signatures

On BioConductor:BulkSignalR-0.99.22(bioc 3.21)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

networkrnaseqsoftwareproteomicstranscriptomicsnetworkinferencespatial

5.22 score 15 scripts 1 downloads 80 exports 179 dependencies

Last updated 22 days agofrom:a707d8a2cd. Checks:5 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 11 2025
R-4.5-winOKJan 11 2025
R-4.5-linuxOKJan 11 2025
R-4.4-winOKJan 11 2025
R-4.4-macOKJan 11 2025

Exports:addClusterCompalluvialPlotassignCellTypesToInteractionsBSRClusterCompBSRDataModelBSRInferenceBSRInferenceCompBSRSignatureBSRSignatureCompbubblePlotPathwaysLRcacheClearcacheInfocacheVersioncellTypeFrequencycellularNetworkcellularNetworkTablechordDiagramLRcoercecolClusterAcolClusterBcomparisoncomparisonNameconvertToHumancreateDatabasecreateResourcesdifferentialStatsfindOrthoGenesgenerateSpatialPlotsgetComplexesgetInteractionsgetLRIntracellNetworkgetLRNetworkgetPathwayStatsgetResourceinferenceParametersinitialOrganisminitialOrthologslearnParametersligandslogTransformedLRinterLRinterScoreLRinterShortmaxLigandSpatialCountsmuncountsnormalizationparameterspathwaysreceptorsreduceToBestPathwayreduceToLigandreduceToPathwayreduceToReceptorrelateToGeneSetremoveClusterComprescoreInferenceresetLRdbresetNetworkresetPathwaysresetToInitialOrganismscoreLRGeneSignaturesscoreSignaturesseparatedLRPlotsignatureHeatmapssimpleHeatmapsmoothSpatialCountssourceComparisonNamespatialAssociationspatialAssociationPlotspatialDiversityPlotspatialIndexPlotspatialPlotsummarizedCellularNetworktgCorrtgExprtgGenestgLogFCtgPvalupdateInference

Dependencies:abindapeaplotaskpassbabelgenebackportsbase64encBiobaseBiocFileCacheBiocGenericsbitbit64bitopsblobbootbroombslibcachemcarcarDatacirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDerivdigestdoBydoParalleldplyrevaluatefansifarverfastmapfilelockfontawesomeforeachFormulafsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggalluvialggfunggplot2ggplotifyggpubrggrepelggsciggsignifggtreeglmnetGlobalOptionsgluegprofiler2gridExtragridGraphicsgrrgtablehighrhmshomologenehtmltoolshtmlwidgetshttrigraphIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magickmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmulttestmunsellnlmenloptrnnetnumDerivopensslorthogenepatchworkpbkrtestpillarpkgconfigplogrplotlyplyrpngpolynomprettyunitsprogresspromisespurrrquantregR.cacheR.methodsS3R.ooR.utilsR6RANNrappdirsRColorBrewerRcppRcppEigenRCurlreadrrepmisrjsonrlangrmarkdownRSQLiterstatixRtsneS4ArraysS4VectorssassscalesshapeSingleCellExperimentSparseArraySparseMSpatialExperimentstablediststringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttidytreetinytextreeiotzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXVectoryamlyulab.utils

BulkSignalR : Inference of ligand-receptor interactions from bulk data or spatial transcriptomics

Jean-Philippe Villemin, Jacques Colinge

Rendered fromBulkSignalR-Differential.Rmdusingknitr::rmarkdownon Jan 11 2025.

Last update: 2024-12-20
Started: 2023-08-14

BulkSignalR : Inference of ligand-receptor interactions from bulk data or spatial transcriptomics

Jean-Philippe Villemin, Jacques Colinge

Rendered fromBulkSignalR-Main.Rmdusingknitr::rmarkdownon Jan 11 2025.

Last update: 2024-12-20
Started: 2023-08-14

Readme and manuals

Help Manual

Help pageTopics
Transform gmt file to dataframe.formatPathwaysFromGmt
Format dataframe according to json input.formatPathwaysFromJson
Read dataframe from txt file.formatPathwaysFromTxt
Add a comparison between two clusters of samplesaddClusterComp addClusterComp,BSRDataModelComp-method
Alluvial plotalluvialPlot
A skinny dataframe used in the spatial workflowannotation.spa
Assign cell types to L-R interactionsassignCellTypesToInteractions
Mouse transcriptomes across tissuesbodyMap.mouse
Definition of the comparison between two clusters of samplesBSRClusterComp
BulkSignalR Cluster Comparison ObjectBSRClusterComp-class
Prepare a BSRDataModel object from expression dataBSRDataModel
BulkSignalR Data Model ObjectBSRDataModel-class
BulkSignalR Data Model Compare ObjectBSRDataModelComp-class
A skinny BSR-dataModel object related to sdc.bsrdm
A skinny BSR-dataModelComp object related to sdc.bsrdm.comp
A skinny BSR-dataModel object related to spatial datasetbsrdm.spa
A skinny BSR-Inference object related to sdc.bsrinf
A skinny BSR-InferenceComp object related to sdc.bsrinf.comp
A skinny BSR-inference object related to bodyMap.mousebsrinf.mouse
A skinny BSR-inference object related to spatial datasetbsrinf.spa
Inference of ligand-receptor interactionsBSRInference
BulkSignalR Inference ObjectBSRInference-class
Inference of ligand-receptor interactions based on regulationBSRInferenceComp
BulkSignalR cluster comparison-based inference objectBSRInferenceComp-class
Extract gene signatures of LR pair activityBSRSignature
BulkSignalR ligand-receptor signature ObjectBSRSignature-class
Extract gene signatures of LR pair activityBSRSignatureComp
BulkSignalR ligand-receptor signature object for cluster comparisonsBSRSignatureComp-class
Bubble Plot to explore LR & PathwaysbubblePlotPathwaysLR
Delete cache content.cacheClear
Get cache content informations..cacheInfo
Check remote files ressources are changed.cacheVersion
Cell type frequencies in relations to gene setscellTypeFrequency
Build a cellular networkcellularNetwork
Build a table describing a cellular networkcellularNetworkTable
Chord Diagram of LR interactions with correlationschordDiagramLR
Convert BSRDataModel to BSRDataModelCompcoerce coerce,BSRDataModel,BSRDataModelComp-method
Cluster A columns accessorcolClusterA colClusterA,BSRClusterComp-method
Cluster B columns accessorcolClusterB colClusterB,BSRClusterComp-method
Comparisons list accessorcomparison comparison,BSRDataModelComp-method
Comparison name accessorcomparisonName comparisonName,BSRInferenceComp-method comparisonName,BSRSignatureComp-method
Transpose to Human Gene NamesconvertToHuman
Fetch the database from internet.createDatabase
Create all resources.createResources
Cluster comparison statistics accessordifferentialStats differentialStats,BSRClusterComp-method
Orthologs Gene NamesfindOrthoGenes
Generate L-R interaction score spatial plots in a foldergenerateSpatialPlots
Retrieve LR complexesgetComplexes
Retrieve LR interactions.getInteractions
Generate a ligand-receptor-downstream signaling networkgetLRIntracellNetwork
Generate a ligand-receptor networkgetLRNetwork
Basic statistics about hit pathwaysgetPathwayStats getPathwayStats,BSRInference-method
Get ressource from the cache.getResource
Immune cell gene signaturesimmune.signatures
Inference parameters accessorinferenceParameters inferenceParameters,BSRInference-method
organism accessorinitialOrganism initialOrganism,BSRDataModel-method
Model parameter accessorinitialOrthologs initialOrthologs,BSRDataModel-method
Training of BulkSignalR model parameterslearnParameters learnParameters,BSRDataModel-method
ligands accessorligands ligands,BSRInference-method ligands,BSRSignature-method
log.transformed accessorlogTransformed logTransformed,BSRDataModel-method
LRinter accessorLRinter LRinter,BSRInference-method
Simplified LRinter accessor with focus on the LR-scoreLRinterScore LRinterScore,BSRInferenceComp-method
Simplified LRinter accessor reporting the essential columnsLRinterShort LRinterShort,BSRInference-method LRinterShort,BSRInferenceComp-method
Get maximal ligand expression at nearby locationsmaxLigandSpatialCounts
Mu accessormu mu,BSRDataModelComp-method
Normalized count matrix accessorncounts ncounts,BSRDataModel-method
Normalization accessornormalization normalization,BSRDataModel-method
A skinny dataframe used in the mouse workflowortholog.dict
Partial EMT gene signaturep.EMT
Model parameter accessorparameters parameters,BSRDataModel-method
pathways accessorpathways pathways,BSRSignature-method
receptors accessorreceptors receptors,BSRInference-method receptors,BSRSignature-method
Keep one pathway per ligand-receptor pairreduceToBestPathway reduceToBestPathway,BSRInference-method reduceToBestPathway,BSRInferenceComp-method
Aggregate the receptors of a same ligandreduceToLigand reduceToLigand,BSRInference-method reduceToLigand,BSRInferenceComp-method
Aggregate ligands and receptors at the pathway levelreduceToPathway reduceToPathway,BSRInference-method reduceToPathway,BSRInferenceComp-method
Aggregate the ligands of a same receptorreduceToReceptor reduceToReceptor,BSRInference-method reduceToReceptor,BSRInferenceComp-method
Relate ligands to a gene setrelateToGeneSet
Remove a comparison from a BSRDataModelComp object.removeClusterComp removeClusterComp,BSRDataModelComp-method
Inference re-scoringrescoreInference rescoreInference,BSRInference-method rescoreInference,BSRInferenceComp-method
Modify LRdb databaseresetLRdb
Import Network from your ownresetNetwork
Import pathways from a file or dataframeresetPathways
Reset gene names to initial organism providen in first instanceresetToInitialOrganism resetToInitialOrganism,BSRInference-method
Score ligand-receptor gene signaturesscoreLRGeneSignatures scoreLRGeneSignatures,BSRDataModel-method scoreLRGeneSignatures,BSRDataModelComp-method
Generic gene signature scoringscoreSignatures
Salivary duct carcinoma transcriptomessdc
Generate separated plots for a L-R interactionseparatedLRPlot
Heatmap function for gene expression of signaturesignatureHeatmaps
Heatmap function for LR scoressimpleHeatmap
Smooth spatial expression datasmoothSpatialCounts
Source comparison name accessorsourceComparisonName sourceComparisonName,BSRInferenceComp-method
Statistical association of scores with area labelsspatialAssociation
Heatmap plot of association of scores with area labelsspatialAssociationPlot
2D-projection of spatial score distributionsspatialDiversityPlot
Generate a visual index of spatial score distributionsspatialIndexPlot
L-R interaction score spatial displayspatialPlot
Build a summary cellular networksummarizedCellularNetwork
Target gene correlations accessortgCorr tgCorr,BSRInference-method tgCorr,BSRSignature-method
Target gene expression accessortgExpr tgExpr,BSRInferenceComp-method tgExpr,BSRSignatureComp-method
Target genes accessortgGenes tgGenes,BSRInference-method tgGenes,BSRSignature-method
Target gene logFC accessortgLogFC tgLogFC,BSRInferenceComp-method tgLogFC,BSRSignatureComp-method
Target gene P-values accessortgPval tgPval,BSRInferenceComp-method tgPval,BSRSignatureComp-method
Tumor microenvironment gene signaturestme.signatures
Inference updatingupdateInference updateInference,BSRInferenceComp-method