Package: xCell2 0.99.107

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:Almog Angel [aut, cre], Dvir Aran [aut]

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xCell2.pdf |xCell2.html✨
xCell2/json (API)
NEWS

# 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

Datasets:

BlueprintEncode.xCell2Ref - Blueprint and ENCODE Projects Reference
DICE_demo.xCell2Ref - Demo xCell2 Reference Object
ImmGenData.xCell2Ref - Immunologic Genome Project Reference
ImmuneCompendium.xCell2Ref - Immune Compendium Reference
LM22.xCell2Ref - LM22 Reference
MouseRNAseqData.xCell2Ref - Mouse RNA-Seq Data Reference
PanCancer.xCell2Ref - PanCancer Reference
TMECompendium.xCell2Ref - Tumor Microenvironment Compendium Reference
TabulaMurisBlood.xCell2Ref - Tabula Muris Blood Reference
TabulaSapiensBlood.xCell2Ref - Tabula Sapiens Blood Reference
dice_demo_ref - Subset of the DICE Reference
mix_demo - Demo Bulk Gene Expression Data

On BioConductor:xCell2-0.99.107(bioc 3.21)

geneexpression transcriptomics microarray rnaseq singlecell differentialexpression immunooncology genesetenrichment

6.01 score 4 stars 15 scripts 13 exports 142 dependencies

Last updated 11 days agofrom:8f2d48ebf6. Checks:5 OK, 2 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 20 2025
R-4.5-win	NOTE	Jan 20 2025
R-4.5-linux	NOTE	Jan 20 2025
R-4.4-win	OK	Jan 20 2025
R-4.4-mac	OK	Jan 20 2025
R-4.3-win	OK	Jan 20 2025
R-4.3-mac	OK	Jan 20 2025

Exports:getDeps getGenesUsed getParams getSignatures getSpillMat setDeps<-setGenesUsed<-setParams<-setSignatures<-setSpillMat<-xCell2Analysis xCell2GetLineage xCell2Train

Dependencies:abind annotate AnnotationDbi AnnotationHub askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 blob bslib cachem cli clipr codetools colorspace cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray digest dplyr edgeR evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel glue graph GSEABase gtable highr hms htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime minpack.lm munsell nlme ontologyIndex openssl pillar pkgconfig plogr plotly plyr png pracma prettyunits progress promises purrr quadprog R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppGSL RcppParallel RcppZiggurat readr reshape reshape2 Rfast rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales SingleCellExperiment singscore snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML xtable XVector yaml

xCell 2.0: Cell Type Enrichment Analysis

Almog Angel & Dvir Aran

Rendered fromxCell2-vignette.Rmdusingknitr::rmarkdownon Jan 20 2025.

Last update: 2025-01-02
Started: 2024-09-06

Citation

Development and contributors

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