Package: scQTLtools
Type: Package
Title: An R package for single-cell eQTL analysis and visualization
Version: 1.0.3
Authors@R: c(
    person(given = "Xiaofeng", 
           family = "Wu",    
           email = "[email protected]", 
           role  = c("aut", "cre", "cph"), 
           comment = c(ORCID = "0009-0003-6254-5575")),
    person(given = "Xin",      
           family = "Huang", 
           email = "[email protected]",   
           role  = c("aut", "cph"),
           comment = c(ORCID = "0009-0005-2755-0357")),
    person(given = "Jingtong", 
           family = "Kang",  
           email = "[email protected]",     
           role = "com",
           comment = c(ORCID = "0009-0008-8343-3456")),
    person(given = "Siwen",    
           family = "Xu",    
           email = "[email protected]",      
           role  = c("aut", "cph"),
           comment = c(ORCID = "0000-0001-7936-0639"))
    )
Description: This package specializes in analyzing and visualizing eQTL at the
    single-cell level. It can read gene expression matrices or Seurat data, or
    SingleCellExperiment object along with genotype data.
Depends: R (>= 4.4.1.0)
Imports:
    ggplot2(>= 3.5.1),
    Matrix (>= 1.7-0),
    stats (>= 4.4.1),
    progress(>= 1.2.3),
    stringr(>= 1.5.1),
    dplyr(>= 1.1.4),
    SeuratObject(>= 5.0.2),
    methods(>= 4.4.1),
    magrittr(>= 2.0.3),
    patchwork(>= 1.2.0),
    DESeq2 (>= 1.45.3),
    VGAM (>= 1.1-11),
    limma (>= 3.61.9),
    biomaRt(>= 2.61.3),
    gamlss (>= 5.4-22),
    SingleCellExperiment(>= 1.27.2),
    SummarizedExperiment(>= 1.32.0),
    GOSemSim(>= 2.31.2)
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    org.Hs.eg.db,
    org.Mm.eg.db,
    org.Ce.eg.db,
    org.At.tair.db,
    testthat (>= 3.2.1.1)
License: MIT + file LICENSE
URL: https://github.com/XFWuCN/scQTLtools
VignetteBuilder: knitr
BugReports: https://github.com/XFWuCN/scQTLtools/issues
biocViews: Software,GeneExpression,GeneticVariability,SNP,
        DifferentialExpression,GenomicVariation,VariantDetection,Genetics,
        FunctionalGenomics,SystemsBiology,Regression,SingleCell,Normalization,
        Visualization
Encoding: UTF-8
RoxygenNote: 7.3.2
LazyData: false
Config/testthat/edition: 3