Package: enrichit
Title: 'C++' Implementations of Functional Enrichment Analysis
Version: 0.2.7
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), design-aware GSEA on RNA-seq counts with
        per-sample gene set scoring, 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, S4Vectors, stats,
        SummarizedExperiment, yulab.utils (> 0.2.1)
LinkingTo: Rcpp, RcppEigen
Suggests: AnnotationDbi, BiasedUrn, clusterProfiler, DESeq2, DOSE,
        fgsea, gson, qvalue, testthat, jsonlite
Encoding: UTF-8
URL: https://yulab-smu.top/biomedical-knowledge-mining-book/
Config/roxygen2/version: 8.1.1
NeedsCompilation: yes
Packaged: 2026-10-28 19:37:03 UTC; root
Author: Guangchuang Yu [aut, cre]
Config/pak/sysreqs: zlib1g-dev
Repository: https://cran.r-universe.dev
Date/Publication: 2026-10-28 05:50:02 UTC
RemoteUrl: https://github.com/cran/enrichit
RemoteRef: HEAD
RemoteSha: 3640c139e323b819a6780eb8d368d8288077c3d8