Package: signatureSearch
Title: Environment for Gene Expression Searching Combined with
        Functional Enrichment Analysis
Version: 1.22.0
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
git_url: https://git.bioconductor.org/packages/signatureSearch
git_branch: RELEASE_3_21
git_last_commit: 8e1d884
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-16 04:01:07 UTC; biocbuild
Author: Yuzhu Duan [aut],
  Brendan Gongol [cre, aut],
  Thomas Girke [aut]
Maintainer: Brendan Gongol <bgong001@ucr.edu>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-04-16 15:32:52 UTC; windows
Archs: x64
