DESCRIPTION

Encoding: UTF-8
Package: ctwas
Type: Package
Title: Adjusting for Genetic Confounders in Transcriptome-Wide Association
  Studies Improves Discovery of Risk Genes of Complex Traits
Date: 2024-12-02
Version: 0.4.21
Authors@R: c(person("Siming","Zhao",role="aut",email="siming.zhao06@gmail.com"),
             person("Wesley","Crouse",role="aut"),
             person("Sheng","Qian",role="aut",email="shengqian@uchicago.edu"),
             person("Kaixuan","Luo",role=c("aut", "cre"),email="kevinlkx@gmail.com"),
             person("Matthew","Stephens",role="aut"),
             person("Xin","He",role="aut"))
Description: Implements the "causal-TWAS" (cTWAS) method
    for identifying causal genes in genome-wide association studies
    (GWAS) described in S. Zhao et al (2024)
    <DOI:10.1038/s41588-023-01648-9>. cTWAS generalizes methods for
    "transcriptome-wide association studies" (TWAS) in that when
    analyzing a gene it adjusts for not only other nearby genes but
    also nearby genetic variants.
URL: https://github.com/xinhe-lab/ctwas/, https://xinhe-lab.github.io/ctwas/
BugReports: https://github.com/xinhe-lab/ctwas/issues
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Imports:
    utils,
    methods,
    stats,
    tools,
    Matrix,
    parallel,
    logging,
    mixsqp,
    magrittr,
    dplyr,
    tidyr,
    ggplot2,
    ggrepel,
    rlang,
    cowplot,
    crayon,
    readr,
    data.table,
    R.utils,
    RSQLite,
    locuszoomr,
    pgenlibr,
    ensembldb,
    AnnotationFilter
Suggests: 
    Rfast,
    enrichR,
    DT,
    htmltools,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0),
    EnsDb.Hsapiens.v86,
    EnsDb.Hsapiens.v75
biocViews:
    Genetics,
    Software
VignetteBuilder: knitr
NeedsCompilation: no
RoxygenNote: 7.3.2
Config/testthat/edition: 3