xbio/DESCRIPTION at main · WangLabCSU/xbio · GitHub

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Package: xbio
Title: Cross-Process Scoring and Linking Framework for Interpreting Biological Associations
Version: 0.0.0.9000
Authors@R:
    person("Yun", "Peng", , "yunyunp96@163.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2801-3332"))
Description: An R package designed to bridge functional
    relationships between biological processes through flexible and extensible
    scoring strategies. It enables users to quantify associations between two
    sets of processes—whether well-characterized, poorly understood, or
    both—based on gene sets, ranked metrics, or threshold-defined signatures. By
    supporting multiple enrichment and similarity-based methods, including
    over-representation analysis (ORA), GSEA variants, and rank-rank
    hypergeometric overlap (RRHO), 'xbio' provides a unified interface for
    inferring potential functional relevance, co-regulation, or shared
    biological roles. This makes it a powerful tool for functional
    interpretation, knowledge transfer, and hypothesis generation in genomics,
    transcriptomics, and systems biology.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
    R (>= 4.2)
Imports:
    AnnotationDbi,
    cli,
    methods,
    rlang,
    S7,
    utils,
    vctrs (>= 0.5.0)
Suggests:
    pillar,
    AnnotationHub,
    biomaRt,
    fgsea,
    KEGGREST,
    testthat (>= 3.0.0)
Enhances:
    GSEABase
URL: https://github.com/Yunuuuu/xbio
BugReports: https://github.com/Yunuuuu/xbio/issues
Collate:
    'annohub.R'
    'bridge-.R'
    'utils-S7.R'
    'bridge-gsea-prerank.R'
    'bridge-gsea-sample.R'
    'db-.R'
    'db-go.R'
    'db-kegg.R'
    'extendr-wrappers.R'
    'geneset-class.R'
    'geneset-methods.R'
    'genesets-class.R'
    'genesets-gs.R'
    'genesets-io.R'
    'genesets-methods.R'
    'import-standalone-assert.R'
    'import-standalone-obj-type.R'
    'import-standalone-pkg.R'
    'import-standalone-tibble.R'
    'repr-genesets.R'
    'repr-matrix.R'
    'repr-metrics.R'
    'repr-threthold.R'
    'tbl-class.R'
    'utils-file.R'
    'utils.R'
    'xbio-package.R'
    'zzz.R'
Config/rextendr/version: 0.3.1.9001
SystemRequirements: Cargo (Rust's package manager), rustc
Config/testthat/edition: 3