Package: xCell2
Type: Package
Title: A Tool for Generic Cell Type Enrichment Analysis
Version: 1.3.0
Authors@R: 
    c(person(given = "Almog", 
             family = "Angel", 
             role = c("aut", "cre"),
             email = "almog.angel@campus.technion.ac.il",
             comment = c(ORCID = "0009-0001-3297-6935")),
             person(given = "Dvir", 
             family = "Aran", 
             role = "aut",
             email = "dviraran@technion.ac.il",
             comment = c(ORCID = "0000-0001-6334-5039")))
Description: 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.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: false
Depends: 
    R (>= 4.0.0)
biocViews: GeneExpression, Transcriptomics, Microarray, RNASeq, SingleCell, DifferentialExpression, ImmunoOncology, GeneSetEnrichment
Imports: 
    SummarizedExperiment,
    SingleCellExperiment,
    Rfast,
    singscore,
    AnnotationHub,
    ontologyIndex,
    tibble,
    dplyr,
    BiocParallel,
    Matrix,
    minpack.lm,
    pracma,
    methods,
    readr,
    magrittr,
    progress,
    quadprog
Suggests:
    testthat,
    knitr,
    rmarkdown,
    ggplot2,
    randomForest,
    tidyr,
    EnhancedVolcano,
    BiocStyle
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://github.com/AlmogAngel/xCell2
BugReports: https://github.com/AlmogAngel/xCell2/issues
git_url: https://git.bioconductor.org/packages/xCell2
git_branch: devel
git_last_commit: c6b6c48
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
