Merging branches

.gitignore

@@ -3,12 +3,20 @@
 .RData
 .Ruserdata
 inst/doc
-GEOexplorer.Rproj
-app.R
+GEOexplorerV1.Rproj
 errors/
 rsconnect/
 r/bioChecks/
 r/createPackageScript/
 r/deploymentScript/
 r/testScripts/
 tests/testthat/test_microarrayGseWithPoorDataQuality.R
+tests/testthat/testGeoAndUserUploadMergingDatasets.R
+tests/testthat/testGeoMergingDatasets.R
+tests/testthat/testGEOMicroarrayData.R
+tests/testthat/testGEORnaSeq.R
+tests/testthat/testLoadingGEODatasetsPerformance.R
+tests/testthat/testUserUploadMergingDatasets.R
+tests/testthat/testUserUploadMicroarrayData.R
+tests/testthat/testuserUploadRnaSeqData.R
+geoSupFiles/

DESCRIPTION

@@ -1,19 +1,23 @@
 Package: GEOexplorer
-Title: GEOexplorer: an R/Bioconductor package for gene expression analysis 
-  and visualisation
-Date: 2021/10/15
-Version: 1.7.1
+Title: GEOexplorer: a webserver for gene expression analysis and visualisation
+Date: 2023/10/11
+Version: 1.7.2
 Authors@R: 
   c(person(given = "Guy",
            family = "Hunt",
            role = c("aut", "cre"),
-           email = "guypwhunt1992@gmail.com",
+           email = "guy.hunt@kcl.ac.uk",
            comment = c(ORCID = "0000-0002-5217-2678")),
     person(given = "Rafael",
            family = "Henkin",
            role = c("ctb", "ths"),
            email = "r.henkin@qmul.ac.uk",
            comment = c(ORCID = "0000-0002-5511-5230")),
+    person(given = "Alfredo",
+           family = "Iacoangeli",
+           role = c("ctb", "ths"),
+           email = "alfredo.iacoangeli@kcl.ac.uk",
+           comment = c(ORCID = "0000-0002-5280-5017")),
     person(given = "Fabrizio",
            family = "Smeraldi",
            role = c("ctb", "ths"),
@@ -24,35 +28,43 @@ Authors@R:
            role = c("ctb", "ths"),
            email = "m.r.barnes@qmul.ac.uk",
            comment = c(ORCID = "0000-0001-9097-7381")))
-Description: GEOexplorer is a Shiny app that enables 
-  exploratory data analysis and differential gene expression 
-  of gene expression analysis on microarray gene expression 
-  datasets held on the GEO database. The outputs are 
-  interactive graphs that enable users to explore the 
-  results of the analysis. The development of GEOexplorer 
-  was made possible because of the excellent code provided 
-  by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).
+Description: GEOexplorer is a webserver and R/Bioconductor package and web application
+  that enables users to perform gene expression analysis. The development of 
+  GEOexplorer was made possible because of the excellent code provided  by 
+  GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).
 License: GPL-3
 Encoding: UTF-8
-LazyData: true
+LazyData: false
 Roxygen: list(markdown = TRUE)
 URL: https://github.com/guypwhunt/GEOexplorer/
 BugReports: https://github.com/guypwhunt/GEOexplorer/issues
-RoxygenNote: 7.1.1.9001
+RoxygenNote: 7.2.3
 biocViews: 
   Software,
   GeneExpression,
   mRNAMicroarray,
   DifferentialExpression,
   Microarray,
-  MicroRNAArray
-Depends: shiny, limma, Biobase, plotly, shinyBS
+  MicroRNAArray,
+  Transcriptomics,
+  RNASeq
+Depends: 
+    shiny,
+    limma,
+    Biobase,
+    plotly,
+    enrichR,
+    R (>= 4.1.0)
 Imports: 
   DT,
+  XML,
+  httr,
+  sva,
+  xfun,
+  edgeR,
   htmltools,
   factoextra,
   heatmaply,
-  maptools,
   pheatmap,
   scales,
   shinyHeatmaply,
@@ -65,12 +77,16 @@ Imports:
   grDevices,
   stats,
   graphics,
-  utils
+  markdown,
+  knitr,
+  utils,
+  xml2,
+  R.utils,
+  readxl,
+  shinycssloaders
 Suggests: 
     rmarkdown,
-    knitr,
     usethis,
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-PackageStatus: Deprecated

NAMESPACE

@@ -3,17 +3,31 @@
 export(loadApp)
 import(Biobase)
 import(ggplot2, except = c(last_plot))
+import(heatmaply)
+import(enrichR)
 import(impute)
 import(limma)
+import(markdown)
 import(pheatmap)
 import(plotly)
+import(shiny)
 import(shiny, except = c(dataTableOutput, renderDataTable))
 import(shinyHeatmaply)
 import(umap)
-importFrom(DT,JS)
 importFrom(DT,dataTableOutput)
 importFrom(DT,renderDataTable)
 importFrom(GEOquery,getGEO)
+importFrom(GEOquery,getGEOSuppFiles)
+importFrom(R.utils,gunzip)
+importFrom(XML,xmlParse)
+importFrom(XML,xmlToList)
+importFrom(car,pointLabel)
+importFrom(edgeR,DGEList)
+importFrom(edgeR,as.matrix.DGEList)
+importFrom(edgeR,calcNormFactors)
+importFrom(edgeR,cpm)
+importFrom(edgeR,filterByExpr)
+importFrom(edgeR,readDGE)
 importFrom(factoextra,fviz_eig)
 importFrom(factoextra,fviz_pca_biplot)
 importFrom(factoextra,fviz_pca_ind)
@@ -29,18 +43,35 @@ importFrom(graphics,par)
 importFrom(graphics,text)
 importFrom(heatmaply,heatmaply)
 importFrom(htmltools,HTML)
-importFrom(maptools,pointLabel)
+importFrom(httr,GET)
+importFrom(knitr,knit)
+importFrom(readxl,read_excel)
 importFrom(scales,label_percent)
-importFrom(shinyBS,addTooltip)
-importFrom(shinyBS,bsTooltip)
 importFrom(shinybusy,add_busy_spinner)
+importFrom(shinycssloaders,withSpinner)
 importFrom(stats,complete.cases)
 importFrom(stats,cor)
 importFrom(stats,model.matrix)
 importFrom(stats,na.omit)
 importFrom(stats,prcomp)
 importFrom(stats,princomp)
 importFrom(stats,quantile)
+importFrom(stringr,str_locate)
 importFrom(stringr,str_remove_all)
+importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
+importFrom(stringr,str_split)
+importFrom(stringr,str_trim)
+importFrom(stringr,str_trunc)
+importFrom(sva,ComBat)
+importFrom(sva,ComBat_seq)
+importFrom(utils,head)
+importFrom(utils,object.size)
+importFrom(utils,read.csv)
+importFrom(utils,read.delim)
+importFrom(utils,tail)
+importFrom(utils,untar)
 importFrom(utils,write.csv)
+importFrom(xfun,file_ext)
+importFrom(xml2,as_list)
+importFrom(xml2,read_xml)

R/app.R

@@ -15,39 +15,15 @@
 #' @importFrom graphics abline boxplot hist par text
 #' @importFrom stats complete.cases cor model.matrix
 #' na.omit prcomp princomp quantile
-#' @importFrom shinyBS bsTooltip addTooltip
+#' @importFrom shinybusy add_busy_spinner
 #' @author Guy Hunt
 #' @return Large Shiny App
 loadApp <- function() {
   ui <- fluidPage(
-    titlePanel("GEOexplorer"),
-    helpText(
-      "GEO2R is an interactive web tool that allows
-    users to compare two or more groups of experimental
-    conditions in a GEO Series to identify genes that
-    are differentially expressed across experimental
-    conditions.
-    GEOexplorer extends GEO2R's functionalities by enabling
-    a richer set of analysis and graphics to be
-    performed/generated from the GEO2R gene expression data.
-    The development of GEOexplorer was made possible
-    because of the excellent code provided by GEO2R
-             (https://www.ncbi.nlm.nih.gov/geo/geo2r/)."
-    ),
-
-    # Source the Side Bar UI Components
-    sourceSideBarUi(),
-    mainPanel(
-      tabsetPanel(
-        type = "tabs",
-        # Source the Dataset Information UI Components
-        sourceDatasetInformationUi(),
-        # Source the Exploratory Data Analysis UI Components
-        sourceExploratoryDataAnalysisUi(),
-        # Source the Differential Gene Expression UI Components
-        sourceDifferentialGeneExpressionAnalysisUi()
-      )
-    )
+    add_busy_spinner(spin = "fading-circle",
+                     height = "100px",
+                     width = "100px"),
+    sourceUi()
   )
 
   server <- function(input, output, session) {