DESCRIPTION

Package: CelliD
Type: Package
Title: Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis
Version: 1.3.1
Authors@R: c(person("Akira", "Cortal", email = "akira.cortal@institutimagine.org",
  role = c("aut", "cre")),  person("Antonio", "Rausell", role= c("aut", "ctb"), email = "antonio.rausell@institutimagine.org"))
Description: CelliD is a clustering-free multivariate statistical method for the robust extraction of per-cell gene signatures from single-cell RNA-seq. 
  CelliD allows unbiased cell identity recognition across different donors, tissues-of-origin, model organisms and single-cell omics protocols. 
  The package can also be used to explore functional pathways enrichment in single cell data. 
Depends:
    R (>= 4.1),
    Seurat (>= 4.0.1),
    SingleCellExperiment
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
Imports:
    Rcpp,
    RcppArmadillo,
    stats,
    utils,
    Matrix,
    tictoc,
    scater,
    stringr,
    irlba,
    data.table,
    glue,
    pbapply,
    umap,
    Rtsne,
    reticulate,
    fastmatch,
    matrixStats,
    ggplot2,
    BiocParallel,
    SummarizedExperiment,
    fgsea
Suggests:
    knitr,
    rmarkdown,
    BiocStyle,
    testthat,
    tidyverse,
    ggpubr,
    destiny,
    ggrepel
VignetteBuilder: knitr
RoxygenNote: 7.1.1
biocViews: RNASeq, SingleCell, DimensionReduction, Clustering, GeneSetEnrichment, GeneExpression, ATACSeq
LinkingTo: Rcpp, RcppArmadillo