DESCRIPTION

Package: pathlinkR
Type: Package
Title: Analyze and interpret RNA-Seq results
Version: 1.3.7
Authors@R: c(
    person("Travis", "Blimkie", email = "travis.m.blimkie@gmail.com", role = "cre", comment = c(ORCID = "0000-0001-8778-8627")),
    person("Andy", "An", email = "andy@hancocklab.com", role = "aut")
    )
Description: pathlinkR is an R package designed to facilitate analysis of 
    RNA-Seq results. Specifically, our aim with pathlinkR was to provide a 
    number of tools which take a list of DE genes and perform different analyses
    on them, aiding with the interpretation of results. Functions are included 
    to perform pathway enrichment, with muliplte databases supported, and tools
    for visualizing these results. Genes can also be used to create and plot 
    protein-protein interaction networks, all from inside of R. 
biocViews: GeneSetEnrichment, Network, Pathways, Reactome, RNASeq, 
    NetworkEnrichment
BiocType: Software
BugReports: https://github.com/hancockinformatics/pathlinkR/issues
License: GPL-3 + file LICENSE
URL: https://github.com/hancockinformatics/pathlinkR
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/testthat/edition: 3
Depends: 
    R (>= 4.4.0)
Imports:
    circlize,
    clusterProfiler,
    ComplexHeatmap,
    dplyr,
    fgsea,
    ggforce,
    ggplot2,
    ggpubr,
    ggraph,
    ggrepel,
    grid,
    igraph,
    purrr,
    sigora,
    stringr,
    tibble,
    tidygraph,
    tidyr,
    vegan,
    visNetwork
Suggests: 
    AnnotationDbi,
    BiocStyle,
    biomaRt,
    covr,
    DESeq2,
    jsonlite,
    knitr,
    org.Hs.eg.db,
    rmarkdown,
    scales,
    testthat (>= 3.0.0),
    vdiffr