DESCRIPTION

Package: signatureSearch
Title: Environment for Gene Expression Searching Combined with Functional
       Enrichment Analysis
Version: 1.15.2
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: 7.3.1
biocViews: Software, GeneExpression, GO, KEGG, NetworkEnrichment,
           Sequencing, Coverage, DifferentialExpression
URL: https://github.com/yduan004/signatureSearch/
BugReports: https://github.com/yduan004/signatureSearch/issues
LazyData: false