# A Tool for Generic Cell Type Enrichment Analysis

## Documentation for package ‘xCell2’ version 1.4.0

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

## 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