Package: scQTLtools
Type: Package
Title: An R package for single-cell eQTL analysis and visualization
Version: 1.0.0
Authors@R: c(
    person(given = "Xiaofeng", 
           family = "Wu",    
           email = "1427972815@qq.com", 
           role  = c("aut", "cre", "cph"), 
           comment = c(ORCID = "0009-0003-6254-5575")),
    person(given = "Xin",      
           family = "Huang", 
           email = "1097567240@qq.com",   
           role  = c("aut", "cph")),
    person(given = "Jingtong", 
           family = "Kang",  
           email = "1203178107@qq.com",     
           role = "com"),
    person(given = "Siwen",    
           family = "Xu",    
           email = "siwxu@gdpu.edu.cn",      
           role  = c("aut", "cph"))
    )
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. It offers a function 
    for cis-eQTL analysis to  detect eQTL within a given range, and another 
    function to fit models with three methods. Using this package, users can 
    also generate single-cell level visualization result.
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
git_url: https://git.bioconductor.org/packages/scQTLtools
git_branch: RELEASE_3_21
git_last_commit: 8c51673
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-17
NeedsCompilation: no
Packaged: 2025-04-17 22:22:00 UTC; biocbuild
Author: Xiaofeng Wu [aut, cre, cph] (ORCID:
    <https://orcid.org/0009-0003-6254-5575>),
  Xin Huang [aut, cph],
  Jingtong Kang [com],
  Siwen Xu [aut, cph]
Maintainer: Xiaofeng Wu <1427972815@qq.com>
Built: R 4.5.0; ; 2025-04-18 05:08:41 UTC; unix
