Package: signatureSearch
Title: Environment for Gene Expression Searching Combined with
        Functional Enrichment Analysis
Version: 1.24.0
Authors@R: c(person("Yuzhu", "Duan", email = "yduan004@ucr.edu",
                    role = c("aut")),
             person("Brendan", "Gongol", email = "bgong001@ucr.edu",
                    role = c("cre", "aut")),
             person("Thomas", "Girke", email = "thomas.girke@ucr.edu",
                    role = "aut"))
Description: This package implements algorithms and data structures for
        performing gene expression signature (GES) searches, and
        subsequently interpreting the results functionally with
        specialized enrichment methods.
Depends: R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db
Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array,
        magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue,
        stats, utils, reshape2, visNetwork, BiocParallel, fastmatch,
        reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5,
        GSEABase, DelayedArray, BiocGenerics, tibble
Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData,
        DT
License: Artistic-2.0
SystemRequirements: C++11
LinkingTo: Rcpp
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 7.2.3
biocViews: Software, GeneExpression, GO, KEGG, NetworkEnrichment,
        Sequencing, Coverage, DifferentialExpression
URL: https://github.com/yduan004/signatureSearch/
BugReports: https://github.com/yduan004/signatureSearch/issues
LazyData: false
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libpng-dev libxml2-dev libssl-dev
        libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:55:44 UTC
RemoteUrl: https://github.com/bioc/signatureSearch
RemoteRef: RELEASE_3_22
RemoteSha: ce6ab959ced593dece51fcf97a59446ac4ba548e
NeedsCompilation: yes
Packaged: 2026-01-04 13:02:24 UTC; root
Author: Yuzhu Duan [aut],
  Brendan Gongol [cre, aut],
  Thomas Girke [aut]
Maintainer: Brendan Gongol <bgong001@ucr.edu>
Built: R 4.5.2; x86_64-w64-mingw32; 2026-01-04 13:06:57 UTC; windows
Archs: x64
