pecotmr/DESCRIPTION at main · StatFunGen/pecotmr · GitHub

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Encoding: UTF-8
Type: Package
Package: pecotmr
Version: 0.9.2
Date: 2026-02-28
Title: Post-GWAS enrichment, colocalization, TWAS and Mendelian Randomization to integrate molecular QTL and GWAS
Description: The majority of the statistical models in pecotmr are based on fine-mapped single effects described in Wang G et al (2020) JRSS-B. It also incorporates wrappers to a series of useful TWAS methods as well as utility functions for QTL and GWAS integration.
URL: https://statfungen.github.io/pecotmr, https://github.com/StatFunGen/pecotmr
BugReports: https://github.com/StatFunGen/pecotmr/issues
Authors@R: c(person("Gao Wang",role = c("cre","aut"),
                  email = "wang.gaow@columbia.edu"),
                  person("Daniel Nachun", role = "aut",
                  email = "dnachun@stanford.edu"),
                  person("StatFunGen Lab", role = "ctb"))
License: MIT + file LICENSE
biocViews:
    StatisticalMethod,
    GenomeWideAssociation,
    SNP,
    Regression,
    Bayesian,
    Genetics,
    FunctionalGenomics,
    GeneExpression,
    LinkageDisequilibrium
Imports:
    archive,
    BiocGenerics,
    BiocParallel,
    Biostrings,
    checkmate,
    coloc,
    colocboost,
    DelayedArray,
    dplyr,
    GenomeInfoDb,
    GenomicRanges,
    glue,
    IRanges,
    magrittr,
    MASS,
    Matrix,
    matrixStats,
    metafor,
    methods,
    MultiAssayExperiment,
    purrr,
    quadprog,
    readr,
    rlang,
    Rsamtools,
    S4Arrays,
    S4Vectors,
    stringr,
    SummarizedExperiment,
    susieR (>= 0.16.4),
    tibble,
    tictoc,
    tidyr,
    tidyselect,
    utils,
    vctrs,
    vroom,
    withr,
    yaml
Suggests:
    arrow,
    aSPU,
    BGLR,
    bigsnpr,
    bigstatsr,
    coda,
    CorShrink,
    ctwas,
    ebnm,
    flashier,
    fsusieR,
    GBJ,
    gdsfmt,
    glmnet,
    harmonicmeanp,
    igraph,
    knitr,
    L0Learn,
    mashr,
    mr.mashr,
    mvsusieR,
    ncvreg,
    nnls,
    pgenlibr,
    plinkQC,
    plyranges,
    poolr,
    qgg,
    qvalue,
    RcppDPR,
    Rfast,
    rmarkdown,
    robustbase,
    rtracklayer,
    SNPRelate,
    snpStats,
    testthat,
    udr,
    VariantAnnotation,
    wavethresh
Remotes:
    kkdey/CorShrink,
    stephenslab/fsusieR,
    stephenslab/mvsusieR,
    stephenslab/susieR,
    stephenslab/udr,
    xinhe-lab/multigroup_ctwas,
LinkingTo:
    cpp11,
    cpp11armadillo
NeedsCompilation: yes
VignetteBuilder: knitr
Config/roxygen2/version: 8.1.0
Collate:
    'AllGenerics.R'
    'RangedTupleList.R'
    'GenotypeHandle.R'
    'AllClasses.R'
    'AnnotationMatrix.R'
    'ColocResult.R'
    'ColocBoostResult.R'
    'tupleSelectors.R'
    'CtwasResult.R'
    'CtwasResultEntry.R'
    'GwasFineMappingResult.R'
    'H2Estimate.R'
    'JointGroup.R'
    'LdBlocks.R'
    'LdData.R'
    'LdStatistic.R'
    'LdEigen.R'
    'LdScore.R'
    'MashPrior.R'
    'MethodOptions.R'
    'MethodParam.R'
    'QtlDataset.R'
    'MultiStudyQtlDataset.R'
    'QtlFineMappingResult.R'
    'SldscData.R'
    'causalInferencePipeline.R'
    'gwasSumStats.R'
    'qtlSumStats.R'
    'fineMappingPipeline.R'
    'ld.R'
    'colocPipeline.R'
    'colocboostPipeline.R'
    'cpp11.R'
    'crossValidation.R'
    'ctwasPipeline.R'
    'ctwasWrapper.R'
    'enloc.R'
    'exampleData.R'
    'fineMappingRow.R'
    'fineMappingWrappers.R'
    'genotypeIo.R'
    'h2Annotations.R'
    'h2EstimationWrappers.R'
    'jointEngine.R'
    'jointSpecification.R'
    'sumstatsQc.R'
    'variantId.R'
    'manifestLoaders.R'
    'mashPipeline.R'
    'mashWrapper.R'
    'overlapTopLoci.R'
    'pvalCombineWrappers.R'
    'qtlAssociationPostprocess.R'
    'qtlEnrichmentPipeline.R'
    'regularizedRegressionWrappers.R'
    'relatednessQc.R'
    'sldscPostprocessingPipeline.R'
    'sldscWrapper.R'
    'twasWeights.R'
    'twasWeightsPipeline.R'
    'twasWeightsRow.R'
    'vcfWriter.R'
Depends:
    R (>= 4.5)
LazyData: false