Package: enrichit
Title: 'C++' Implementations of Functional Enrichment Analysis
Version: 0.2.0
Authors@R: person(given = "Guangchuang", family = "Yu",
               email = "guangchuangyu@gmail.com", role  = c("aut", "cre"))
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Description: Fast implementations of functional enrichment analysis
        methods using 'C++' via 'Rcpp'. Currently provides
        Over-Representation Analysis (ORA), Gene Set Enrichment
        Analysis (GSEA), Weighted Enrichment Analysis for ORA and GSEA,
        Network-based Set Enrichment Analysis (NSEA), multi-layer
        network-based enrichment, and multi-omics integration
        workflows. Additional features include early fusion at the
        feature level, late fusion at the pathway level, multi-omics
        contribution tracing, topology-aware explanation helpers,
        Bayesian term selection, and extremely fast Random Walk with
        Restart (RWR) using 'RcppEigen'. The enrichment methods build
        on GSEA by Subramanian et al. (2005)
        <doi:10.1073/pnas.0506580102>, the multilevel strategy derived
        from 'fgsea' by Korotkevich et al. (2021) <doi:10.1101/060012>,
        and network-based enrichment ideas described by Glaab et al.
        (2012) <doi:10.1093/bioinformatics/bts389>.
License: Artistic-2.0
Depends: R (>= 3.5.0)
Imports: Matrix, methods, Rcpp (>= 1.0.10), rlang, stats, yulab.utils
        (> 0.2.1)
LinkingTo: Rcpp, RcppEigen
Suggests: AnnotationDbi, BiasedUrn, clusterProfiler, DOSE, fgsea, gson,
        qvalue, testthat
Encoding: UTF-8
URL: https://yulab-smu.top/biomedical-knowledge-mining-book/
Config/roxygen2/version: 8.0.0
NeedsCompilation: yes
Packaged: 2026-07-02 21:26:18 UTC; root
Author: Guangchuang Yu [aut, cre]
Repository: https://cran.r-universe.dev
Date/Publication: 2026-07-01 22:50:15 UTC
RemoteUrl: https://github.com/cran/enrichit
RemoteRef: HEAD
RemoteSha: fb787911b606956438ea0245139709d1adc5214d