Package: xCell2 1.5.0
Almog Angel
xCell2: A Tool for Generic Cell Type Enrichment Analysis
xCell2 provides methods for cell type enrichment analysis using cell type signatures. It includes three main functions - 1. xCell2Train for training custom references objects from bulk or single-cell RNA-seq datasets. 2. xCell2Analysis for conducting the cell type enrichment analysis using the custom reference. 3. xCell2GetLineage for identifying dependencies between different cell types using ontology.
Authors:
xCell2_1.5.0.tar.gz
xCell2_1.5.0.zip(r-4.7-any)xCell2_1.5.0.zip(r-4.6-any)xCell2_1.5.0.zip(r-4.5-any)
xCell2_1.5.0.tgz(r-4.6-any)xCell2_1.5.0.tgz(r-4.5-any)
xCell2_1.5.0.tar.gz(r-4.7-any)xCell2_1.5.0.tar.gz(r-4.6-any)
xCell2_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
xCell2/json (API)
| # Install 'xCell2' in R: |
| install.packages('xCell2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/almogangel/xcell2/issues
- BlueprintEncode.xCell2Ref - Blueprint and ENCODE Projects Reference
- dice_demo_ref - Subset of the DICE Reference
- DICE_demo.xCell2Ref - Demo xCell2 Reference Object
- 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
- TabulaMurisBlood.xCell2Ref - Tabula Muris Blood Reference
- TabulaSapiensBlood.xCell2Ref - Tabula Sapiens Blood Reference
- TMECompendium.xCell2Ref - Tumor Microenvironment Compendium Reference
On BioConductor:xCell2-1.5.0(bioc 3.24)xCell2-1.4.0(bioc 3.23)
geneexpressiontranscriptomicsmicroarrayrnaseqsinglecelldifferentialexpressionimmunooncologygenesetenrichment
Last updated from:6cf1ed07d5. Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 219 | ||
| linux-devel | ERROR | 461 | ||
| source / vignettes | ERROR | 304 | ||
| linux-release | ERROR | 503 | ||
| macos-release | ERROR | 249 | ||
| macos-oldrel | ERROR | 311 | ||
| windows-devel | ERROR | 344 | ||
| windows-release | ERROR | 339 | ||
| windows-oldrel | ERROR | 343 | ||
| wasm-release | OK | 157 |
Exports:getDepsgetGenesUsedgetParamsgetSignaturesgetSpillMatsetDeps<-setGenesUsed<-setParams<-setSignatures<-setSpillMat<-xCell2AnalysisxCell2GetLineagexCell2Train
Dependencies:abindannotateAnnotationDbiAnnotationHubaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobbslibcachemclicliprcodetoolscpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyredgeRevaluatefarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggrepelgluegraphGSEABasegtablehighrhmshtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeminpack.lmontologyIndexopensslotelpillarpkgconfigplotlyplyrpngpracmaprettyunitsprogresspromisespurrrquadprogR6rappdirsRColorBrewerRcppRcppArmadilloRcppParallelreadrreshapereshape2RfastrlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesSeqinfoSingleCellExperimentsingscoresnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunXMLxtableXVectoryamlzigg
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Blueprint and ENCODE Projects Reference | BlueprintEncode.xCell2Ref |
| Access Cell Type Dependencies | dependencies getDeps getDeps,xCell2Object-method setDeps<- setDeps<-,xCell2Object-method |
| Subset of the DICE Reference | dice_demo_ref |
| Demo xCell2 Reference Object | DICE_demo.xCell2Ref |
| Access Genes Used | genesUsed getGenesUsed getGenesUsed,xCell2Object-method setGenesUsed<- setGenesUsed<-,xCell2Object-method |
| Immunologic Genome Project Reference | ImmGenData.xCell2Ref |
| Immune Compendium Reference | ImmuneCompendium.xCell2Ref |
| LM22 Reference | LM22.xCell2Ref |
| Demo Bulk Gene Expression Data | mix_demo |
| Mouse RNA-Seq Data Reference | MouseRNAseqData.xCell2Ref |
| PanCancer Reference | PanCancer.xCell2Ref |
| Access Transformation Parameters | getParams getParams,xCell2Object-method params setParams<- setParams<-,xCell2Object-method |
| Access Cell Type Signatures | getSignatures getSignatures,xCell2Object-method setSignatures<- setSignatures<-,xCell2Object-method signatures |
| Access Spillover Matrix | getSpillMat getSpillMat,xCell2Object-method setSpillMat<- setSpillMat<-,xCell2Object-method spillMat |
| Tabula Muris Blood Reference | TabulaMurisBlood.xCell2Ref |
| Tabula Sapiens Blood Reference | TabulaSapiensBlood.xCell2Ref |
| Tumor Microenvironment Compendium Reference | TMECompendium.xCell2Ref |
| Perform Cell Type Enrichment Analysis | xCell2Analysis |
| Identify Cell Type Lineage Dependencies | xCell2GetLineage |
| xCell2Object Class | xCell2Object-class |
| Train Custom xCell2 Reference Object | xCell2Train |