DESCRIPTION

Package: pQTLtools
Type: Package
Title: A Protein Quantitative Trait Locus Toolkit
Version: 0.4
Date: 2024-11-20
Authors@R: c(
    person("Jing Hua", "Zhao", , "jinghuazhao@hotmail.com", role = c("aut", "cre"),
      comment = c(ORCID = "0000-0002-1463-5870", "0000-0003-4930-3582")
    ),
    person("Jimmy", "Peters", role = "aut"),
    person("Bram", "Prins", role = "aut")
  )
Description: It collects data and utilities for pQTL analysis, including
  1. Protein GWAS facilities such as Manhattan/QQ/LocusZoom.js plots, novelty/consequence checking;
  2. Articles linking functions for cis/trans classification, pQTL-gene plot, 2d/3d-plotly plots, forest plots among others available from gap, <https://cran.r-project.org/package=gap>, as well as colocalization, pQTL-Mendelian Randomization via TwoSampleMR. <https://mrcieu.github.io/TwoSampleMR/>;
  3. Query on genes, regions, and SNPs via PhenoScanner, <http://www.phenoscanner.medschl.cam.ac.uk/>.
  4. Mapping of UniProt IDs to other resources;
  5. Showcases of Bioconductor, <https://github.com/bioconductor>, and snakemake, <https://github.com/snakemake>.
License: MIT + file LICENSE
URL: https://github.com/jinghuazhao/pQTLtools
BugReports: https://github.com/jinghuazhao/pQTLtools/issues
Depends:
    R (>= 3.5.0), pQTLdata
Imports: dplyr, gap, ggplot2, Rdpack
RdMacros: Rdpack
Suggests:
    AnnotationFilter,
    Biobase,
    Biostrings,
    ComplexHeatmap,
    DESeq2,
    EnsDb.Hsapiens.v86,
    FlowSorted.DLPFC.450k,
    GeneNet,
    GenomicFeatures,
    GenomeInfoDb,
    GenomicRanges,
    IlluminaHumanMethylation450kmanifest,
    IRanges,
    OUTRIDER,
    RColorBrewer,
    RMariaDB,
    Rgraphviz,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    VariantAnnotation,
    arrayQualityMetrics,
    biomaRt,
    bladderbatch,
    bookdown,
    circlize,
    clusterProfiler,
    coloc,
    corpcor,
    cowplot,
    doParallel,
    ensembldb,
    fdrtool,
    gap.datasets,
    graph,
    graphite,
    heatmaply,
    htmltools,
    htmlwidgets,
    httr,
    ieugwasr,
    karyoploteR,
    knitr,
    meta,
    mclust,
    minfi,
    openxlsx,
    org.Hs.eg.db,
    plyr,
    plotly,
    purrr,
    quantro,
    readr,
    recount3,
    regioneR,
    reticulate,
    rGREAT,
    rgl,
    rmarkdown,
    rtracklayer,
    scatterplot3d,
    seqminer,
    stringr,
    tourr,
    sva,
    gwasvcf,
    TwoSampleMR,
    phenoscanner
Remotes:
    mrcieu/gwasvcf,
    mrcieu/TwoSampleMR,
    phenoscanner/phenoscanner
VignetteBuilder: knitr
LazyData: Yes
LazyLoad: Yes
LazyDataCompression: xz
NeedsCompilation: no
Encoding: UTF-8
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)