DESCRIPTION

Package: tkoi
Title: Transcriptomic Knowledge-Graph Omics Integration for Human Pathway Analysis
Version: 1.0.0
Authors@R: 
    person("Wanjun", "Gu", ,email = "wanjun.gu@ucsf.edu", role = c("aut", "cre"), 
           comment = c(ORCID = "0000-0002-7342-7000"))
Description: A system for enriching biological concepts and integrating transcriptomic data with a 
    human-specific heterogeneous biological knowledge graph from transcriptomics data. It enables advanced analyses, including pathway enrichment, network-based gene ranking, and functional annotation. Key features include personalized PageRank computation, visualization of network enrichment, and seamless integration with biological ontologies. The package is designed for users in 
    genomics and computational biology to gain insights from large-scale transcriptomic data.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: 
    clusterProfiler,
    data.table,
    dplyr,
    enrichplot,
    ggplot2,
    glue,
    grDevices,
    igraph,
    knitr,
    org.Hs.eg.db,
    purrr,
    readxl,
    RNOmni,
    scales,
    sodium,
    stats,
    utils,
    writexl
Depends: 
    R (>= 3.5)
LazyData: true
Suggests: 
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr