Merge pull request #15 from LUMC/develop

Develop

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dgeAnalysis
 Type: Package
 Title: dgeAnalysis
-Version: 1.3.2
+Version: 1.4.1
 Author@R:
   person("Tom", "Kuipers", email = "t.b.kuipers@outlook.com", role = c("aut", "cre"))
 Description:
@@ -19,23 +19,17 @@ Imports:
     shinyjs (>= 2.0.0),
     BiocManager (>= 1.30.10),
     knitr (>= 1.30),
-    tidyr (>= 1.1.2),
-    scales (>= 1.1.1),
-    broom (>= 0.7.1),
-    plotly (>= 4.9.2),
-    igraph (>= 1.2.5),
-    reshape2 (>= 1.4.4),
     SummarizedExperiment (>= 1.18.2),
     edgeR (>= 3.30.3),
     limma (>= 3.44.3),
     DESeq2 (>= 1.28.1),
-    clusterProfiler (>= 3.16.1),
-    DOSE (>= 3.14.0),
-    graphite (>= 1.34.0),
-    ReactomePA (>= 1.32.0),
-    org.Hs.eg.db (>= 3.11.4),
-    org.Mm.eg.db (>= 3.11.4),
+    tidyr (>= 1.1.2),
+    scales (>= 1.1.1),
+    broom (>= 0.7.1),
+    plotly (>= 4.9.2),
     rmarkdown (>= 2.4),
+    gprofiler2 (>= 0.2.0),
+    igraph (>= 1.2.5),
     WGCNA (>= 1.69)
 biocViews: Annotation, Clustering, GeneSetEnrichment, GO, KEGG,
     MultipleComparison, Pathways, Reactome, Visualization,

NAMESPACE

@@ -15,14 +15,13 @@ export(createContrast)
 export(createDesign)
 export(createMatrix)
 export(deRatioPlot)
-export(emap_plotly)
 export(enrichBarplot)
+export(enrichDE)
 export(extract_geneSets)
 export(gamConfidenceFit)
 export(geneStrandBar)
 export(getCount)
 export(get_dendrogram_data)
-export(get_geneList)
 export(get_organismID)
 export(heatplotly)
 export(informationBox)
@@ -31,7 +30,6 @@ export(list2graph)
 export(ma_plot)
 export(multidimensionalScaling2dPlot)
 export(multidimensionalScaling3dPlot)
-export(overlap_ratio)
 export(pValuePlot)
 export(plot_module_trait_relation_heat)
 export(plot_modules)
@@ -48,7 +46,6 @@ export(samplePca3dPlot)
 export(stackDge)
 export(startApp)
 export(topDgeHeatmapPlot)
-export(update_n)
 export(variableHeatmapPlot)
 export(variancePcaPlot)
 export(volcanoPlot)