xCell2

[AlmogAngel]

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• Repository: https://github.com/AlmogAngel/xCell2

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[bioc-issue-bot]

Hi @AlmogAngel

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: xCell2
Type: Package
Title: A Tool for Generic Cell Type Enrichment Analysis
Version: 0.99.0
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")))
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 (>= 4.4.0)
biocViews: GeneExpression, Transcriptomics, Microarray, RNASeq, SingleCell, DifferentialExpression, ImmunoOncology, GeneSetEnrichment
Imports: 
    Rfast,
    singscore,
    ontoProc (>= 1.26.4),
    ontologyIndex,
    tibble,
    dplyr,
    BiocParallel,
    Matrix,
    minpack.lm,
    pracma,
    methods,
    readr,
    tidyr
Suggests:
    devtools,
    knitr,
    rmarkdown,
    testthat
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://github.com/AlmogAngel/xCell2
BugReports: https://github.com/AlmogAngel/xCell2/issues

[lshep]

Please remove the doc directory. These files should be created automatically through the R CMD build process.

If this package is working with gene expression it should also be able to use SummarizedExperiments/SingleCellExperiments; the standard Bioconductor class object for such data. Is there a reason it does not?