Package: signatureSearch Title: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis Version: 1.27.0 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(>= 4.5.0), 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, readr, rhdf5, GSEABase, DelayedArray, GO.db, BiocGenerics, tibble, DOSE, AnnotationHub, stringr Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 SystemRequirements: C++20 LinkingTo: Rcpp Encoding: UTF-8 VignetteBuilder: knitr RoxygenNote: 7.3.3 biocViews: Software, GeneExpression, GO, NetworkEnrichment, Sequencing, Coverage, DifferentialExpression URL: https://github.com/yduan004/signatureSearch/ BugReports: https://github.com/yduan004/signatureSearch/issues LazyData: false Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:51:25 UTC RemoteUrl: https://github.com/bioc/signatureSearch RemoteRef: HEAD RemoteSha: fd4dd95f4ac1d65555fb61906412b1486f60ca9e NeedsCompilation: yes Packaged: 2026-06-23 19:41:06 UTC; root Author: Yuzhu Duan [aut], Brendan Gongol [cre, aut], Thomas Girke [aut] Maintainer: Brendan Gongol