A Tool for Generic Cell Type Enrichment Analysis

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Documentation for package ‘xCell2’ version 1.1.0

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

Help Pages

BlueprintEncode.xCell2Ref	Blueprint and ENCODE Projects Reference
dependencies	Access Cell Type Dependencies
DICE_demo.xCell2Ref	Demo xCell2 Reference Object
dice_demo_ref	Subset of the DICE Reference
genesUsed	Access Genes Used
getDeps	Access Cell Type Dependencies
getDeps-method	Access Cell Type Dependencies
getGenesUsed	Access Genes Used
getGenesUsed-method	Access Genes Used
getParams	Access Transformation Parameters
getParams-method	Access Transformation Parameters
getSignatures	Access Cell Type Signatures
getSignatures-method	Access Cell Type Signatures
getSpillMat	Access Spillover Matrix
getSpillMat-method	Access Spillover Matrix
ImmGenData.xCell2Ref	Immunologic Genome Project Reference
ImmuneCompendium.xCell2Ref	Immune Compendium Reference
LM22.xCell2Ref	LM22 Reference
mix_demo	Demo Bulk Gene Expression Data
MouseRNAseqData.xCell2Ref	Mouse RNA-Seq Data Reference
PanCancer.xCell2Ref	PanCancer Reference
params	Access Transformation Parameters
setDeps<-	Access Cell Type Dependencies
setDeps<--method	Access Cell Type Dependencies
setGenesUsed<-	Access Genes Used
setGenesUsed<--method	Access Genes Used
setParams<-	Access Transformation Parameters
setParams<--method	Access Transformation Parameters
setSignatures<-	Access Cell Type Signatures
setSignatures<--method	Access Cell Type Signatures
setSpillMat<-	Access Spillover Matrix
setSpillMat<--method	Access Spillover Matrix
signatures	Access Cell Type Signatures
spillMat	Access Spillover Matrix
TabulaMurisBlood.xCell2Ref	Tabula Muris Blood Reference
TabulaSapiensBlood.xCell2Ref	Tabula Sapiens Blood Reference
TMECompendium.xCell2Ref	Tumor Microenvironment Compendium Reference
xCell2Analysis	Perform Cell Type Enrichment Analysis
xCell2GetLineage	Identify Cell Type Lineage Dependencies
xCell2Object-class	xCell2Object Class
xCell2Train	Train Custom xCell2 Reference Object