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Credit goes to code.bioconductor.org

  1. shinyDSP
  2. NAMESPACE
Browse code

Peer review fix: enabled paging, adj. P val cutoff, removed 'turbo' and added all 115 palettes under hcl.pals()

kimsjune authored on 11/06/2025 03:17:29
Showing 1 changed files
NAMESPACE
History View file @ 1a01b71
... ... 
@@ -67,6 +67,7 @@ importFrom(ggpubr,get_legend)
67 67 
 importFrom(ggrepel,geom_text_repel)
68 68 
 importFrom(grDevices,colors)
69 69 
 importFrom(grDevices,dev.off)
70 
+importFrom(grDevices,hcl.pals)
70 71 
 importFrom(grDevices,png)
71 72 
 importFrom(grid,gpar)
72 73 
 importFrom(grid,unit)
Browse code

Added GHA. R CMD build/pass no errors or warnings.

kimsjune authored on 26/10/2024 20:12:26
Showing 1 changed files
NAMESPACE
History View file @ c352871
... ... 
@@ -138,6 +138,7 @@ importFrom(stats,setNames)
138 138 
 importFrom(stringr,str_split_1)
139 139 
 importFrom(tibble,num)
140 140 
 importFrom(tibble,rownames_to_column)
141 
+importFrom(tidyr,unite)
141 142 
 importFrom(utils,combn)
142 143 
 importFrom(utils,de)
143 144 
 importFrom(utils,globalVariables)
Browse code

Implemented shinytest2. Abandoned 'expect_values()' in favour of 'expect_screenshot()'. Added vignette boilerplate.

kimsjune authored on 25/10/2024 20:33:19
Showing 1 changed files
NAMESPACE
History View file @ 2bb822f
... ... 
@@ -65,12 +65,15 @@ importFrom(ggplot2,ylim)
65 65 
 importFrom(ggpubr,as_ggplot)
66 66 
 importFrom(ggpubr,get_legend)
67 67 
 importFrom(ggrepel,geom_text_repel)
68 
+importFrom(grDevices,colors)
68 69 
 importFrom(grDevices,dev.off)
69 70 
 importFrom(grDevices,png)
70 71 
 importFrom(grid,gpar)
71 72 
 importFrom(grid,unit)
73 
+importFrom(htmltools,HTML)
72 74 
 importFrom(htmltools,div)
73 75 
 importFrom(htmltools,h4)
76 
+importFrom(htmltools,span)
74 77 
 importFrom(htmltools,tagList)
75 78 
 importFrom(limma,contrasts.fit)
76 79 
 importFrom(limma,duplicateCorrelation)
... ... 
@@ -83,9 +86,10 @@ importFrom(limma,voom)
83 86 
 importFrom(magrittr,"%>%")
84 87 
 importFrom(pals,alphabet)
85 88 
 importFrom(pals,alphabet2)
89 
+importFrom(pals,cols25)
86 90 
 importFrom(pals,glasbey)
91 
+importFrom(pals,watlington)
87 92 
 importFrom(readr,read_delim)
88 
-importFrom(readxl,read_excel)
89 93 
 importFrom(scales,number_format)
90 94 
 importFrom(scales,scientific)
91 95 
 importFrom(scater,runPCA)
... ... 
@@ -97,6 +101,7 @@ importFrom(shiny,eventReactive)
97 101 
 importFrom(shiny,fluidRow)
98 102 
 importFrom(shiny,icon)
99 103 
 importFrom(shiny,numericInput)
104 
+importFrom(shiny,observe)
100 105 
 importFrom(shiny,observeEvent)
101 106 
 importFrom(shiny,radioButtons)
102 107 
 importFrom(shiny,reactive)
... ... 
@@ -120,11 +125,15 @@ importFrom(shinyjs,hide)
120 125 
 importFrom(shinyjs,show)
121 126 
 importFrom(shinyjs,toggle)
122 127 
 importFrom(shinyjs,useShinyjs)
128 
+importFrom(shinyvalidate,InputValidator)
129 
+importFrom(shinyvalidate,sv_in_set)
130 
+importFrom(shinyvalidate,sv_required)
123 131 
 importFrom(standR,findNCGs)
124 132 
 importFrom(standR,geomxBatchCorrection)
125 133 
 importFrom(standR,geomxNorm)
126 134 
 importFrom(standR,readGeoMx)
127 135 
 importFrom(stats,model.matrix)
136 
+importFrom(stats,quantile)
128 137 
 importFrom(stats,setNames)
129 138 
 importFrom(stringr,str_split_1)
130 139 
 importFrom(tibble,num)
... ... 
@@ -132,6 +141,8 @@ importFrom(tibble,rownames_to_column)
132 141 
 importFrom(utils,combn)
133 142 
 importFrom(utils,de)
134 143 
 importFrom(utils,globalVariables)
144 
+importFrom(utils,packageDescription)
145 
+importFrom(utils,tail)
135 146 
 importFrom(utils,write.csv)
136 147 
 importFrom(utils,write.table)
137 148 
 importFrom(withr,with_options)
Browse code

Fixed PCA plots. Removed redundant validation messages.

kimsjune authored on 24/10/2024 03:26:13
Showing 1 changed files
NAMESPACE
History View file @ 3d5e8ab
... ... 
@@ -87,6 +87,7 @@ importFrom(pals,glasbey)
87 87 
 importFrom(readr,read_delim)
88 88 
 importFrom(readxl,read_excel)
89 89 
 importFrom(scales,number_format)
90 
+importFrom(scales,scientific)
90 91 
 importFrom(scater,runPCA)
91 92 
 importFrom(shiny,addResourcePath)
92 93 
 importFrom(shiny,column)
Browse code

Implementing QC. Scatterplots can be generated. In progress.

kimsjune authored on 23/10/2024 21:53:41
Showing 1 changed files
NAMESPACE
History View file @ 824e6ce
... ... 
@@ -71,6 +71,7 @@ importFrom(grid,gpar)
71 71 
 importFrom(grid,unit)
72 72 
 importFrom(htmltools,div)
73 73 
 importFrom(htmltools,h4)
74 
+importFrom(htmltools,tagList)
74 75 
 importFrom(limma,contrasts.fit)
75 76 
 importFrom(limma,duplicateCorrelation)
76 77 
 importFrom(limma,eBayes)
... ... 
@@ -80,6 +81,9 @@ importFrom(limma,makeContrasts)
80 81 
 importFrom(limma,topTable)
81 82 
 importFrom(limma,voom)
82 83 
 importFrom(magrittr,"%>%")
84 
+importFrom(pals,alphabet)
85 
+importFrom(pals,alphabet2)
86 
+importFrom(pals,glasbey)
83 87 
 importFrom(readr,read_delim)
84 88 
 importFrom(readxl,read_excel)
85 89 
 importFrom(scales,number_format)
... ... 
@@ -120,6 +124,7 @@ importFrom(standR,geomxBatchCorrection)
120 124 
 importFrom(standR,geomxNorm)
121 125 
 importFrom(standR,readGeoMx)
122 126 
 importFrom(stats,model.matrix)
127 
+importFrom(stats,setNames)
123 128 
 importFrom(stringr,str_split_1)
124 129 
 importFrom(tibble,num)
125 130 
 importFrom(tibble,rownames_to_column)
Browse code

Added logic for heatmaps, but there are inaccuracies...

kimsjune authored on 22/10/2024 21:43:43
Showing 1 changed files
NAMESPACE
History View file @ 434ff1b
... ... 
@@ -34,6 +34,7 @@ importFrom(cowplot,plot_grid)
34 34 
 importFrom(cowplot,save_plot)
35 35 
 importFrom(dplyr,across)
36 36 
 importFrom(dplyr,case_when)
37 
+importFrom(dplyr,ensym)
37 38 
 importFrom(dplyr,filter)
38 39 
 importFrom(dplyr,pull)
39 40 
 importFrom(dplyr,select)
... ... 
@@ -119,6 +120,7 @@ importFrom(standR,geomxBatchCorrection)
119 120 
 importFrom(standR,geomxNorm)
120 121 
 importFrom(standR,readGeoMx)
121 122 
 importFrom(stats,model.matrix)
123 
+importFrom(stringr,str_split_1)
122 124 
 importFrom(tibble,num)
123 125 
 importFrom(tibble,rownames_to_column)
124 126 
 importFrom(utils,combn)
Browse code

Saved reactive statements into reactiveValues() pt 2. Consolidated R scripts and make it more tidy.

kimsjune authored on 22/10/2024 05:37:55
Showing 1 changed files
NAMESPACE
History View file @ 6aedb36
... ... 
@@ -21,8 +21,11 @@ importFrom(bslib,css)
21 21 
 importFrom(bslib,layout_columns)
22 22 
 importFrom(bslib,layout_sidebar)
23 23 
 importFrom(bslib,nav_hide)
24 
+importFrom(bslib,nav_item)
25 
+importFrom(bslib,nav_menu)
24 26 
 importFrom(bslib,nav_panel)
25 27 
 importFrom(bslib,nav_show)
28 
+importFrom(bslib,nav_spacer)
26 29 
 importFrom(bslib,page_fillable)
27 30 
 importFrom(bslib,page_navbar)
28 31 
 importFrom(bslib,sidebar)
... ... 
@@ -102,6 +105,7 @@ importFrom(shiny,tabPanel)
102 105 
 importFrom(shiny,tabsetPanel)
103 106 
 importFrom(shiny,tags)
104 107 
 importFrom(shiny,textInput)
108 
+importFrom(shiny,textOutput)
105 109 
 importFrom(shiny,uiOutput)
106 110 
 importFrom(shinyWidgets,radioGroupButtons)
107 111 
 importFrom(shinycssloaders,withSpinner)
Browse code

Working state save

kimsjune authored on 21/10/2024 14:14:05
Showing 1 changed files
NAMESPACE
History View file @ 6774493
... ... 
@@ -35,6 +35,7 @@ importFrom(dplyr,filter)
35 35 
 importFrom(dplyr,pull)
36 36 
 importFrom(dplyr,select)
37 37 
 importFrom(dplyr,slice_head)
38 
+importFrom(dplyr,where)
38 39 
 importFrom(edgeR,SE2DGEList)
39 40 
 importFrom(edgeR,estimateDisp)
40 41 
 importFrom(edgeR,filterByExpr)
... ... 
@@ -86,6 +87,7 @@ importFrom(shiny,downloadHandler)
86 87 
 importFrom(shiny,eventReactive)
87 88 
 importFrom(shiny,fluidRow)
88 89 
 importFrom(shiny,icon)
90 
+importFrom(shiny,numericInput)
89 91 
 importFrom(shiny,observeEvent)
90 92 
 importFrom(shiny,radioButtons)
91 93 
 importFrom(shiny,reactive)
... ... 
@@ -96,7 +98,10 @@ importFrom(shiny,renderUI)
96 98 
 importFrom(shiny,runApp)
97 99 
 importFrom(shiny,selectInput)
98 100 
 importFrom(shiny,sliderInput)
101 
+importFrom(shiny,tabPanel)
102 
+importFrom(shiny,tabsetPanel)
99 103 
 importFrom(shiny,tags)
104 
+importFrom(shiny,textInput)
100 105 
 importFrom(shiny,uiOutput)
101 106 
 importFrom(shinyWidgets,radioGroupButtons)
102 107 
 importFrom(shinycssloaders,withSpinner)
... ... 
@@ -114,5 +119,7 @@ importFrom(tibble,num)
114 119 
 importFrom(tibble,rownames_to_column)
115 120 
 importFrom(utils,combn)
116 121 
 importFrom(utils,de)
122 
+importFrom(utils,globalVariables)
123 
+importFrom(utils,write.csv)
117 124 
 importFrom(utils,write.table)
118 125 
 importFrom(withr,with_options)
Browse code

Added download buttons, pairwise comparison tables and tabs within nav_panel().

kimsjune authored on 21/10/2024 02:08:16
Showing 1 changed files
NAMESPACE
History View file @ f4ab4bf
... ... 
@@ -17,6 +17,7 @@ importFrom(SummarizedExperiment,colData)
17 17 
 importFrom(bsicons,bs_icon)
18 18 
 importFrom(bslib,accordion)
19 19 
 importFrom(bslib,accordion_panel)
20 
+importFrom(bslib,css)
20 21 
 importFrom(bslib,layout_columns)
21 22 
 importFrom(bslib,layout_sidebar)
22 23 
 importFrom(bslib,nav_hide)
... ... 
@@ -28,6 +29,9 @@ importFrom(bslib,sidebar)
28 29 
 importFrom(circlize,colorRamp2)
29 30 
 importFrom(cowplot,plot_grid)
30 31 
 importFrom(cowplot,save_plot)
32 
+importFrom(dplyr,across)
33 
+importFrom(dplyr,case_when)
34 
+importFrom(dplyr,filter)
31 35 
 importFrom(dplyr,pull)
32 36 
 importFrom(dplyr,select)
33 37 
 importFrom(dplyr,slice_head)
... ... 
@@ -38,6 +42,7 @@ importFrom(ggplot2,aes)
38 42 
 importFrom(ggplot2,geom_hline)
39 43 
 importFrom(ggplot2,geom_point)
40 44 
 importFrom(ggplot2,geom_vline)
45 
+importFrom(ggplot2,ggsave)
41 46 
 importFrom(ggplot2,ggtitle)
42 47 
 importFrom(ggplot2,guides)
43 48 
 importFrom(ggplot2,labs)
... ... 
@@ -60,6 +65,7 @@ importFrom(grDevices,png)
60 65 
 importFrom(grid,gpar)
61 66 
 importFrom(grid,unit)
62 67 
 importFrom(htmltools,div)
68 
+importFrom(htmltools,h4)
63 69 
 importFrom(limma,contrasts.fit)
64 70 
 importFrom(limma,duplicateCorrelation)
65 71 
 importFrom(limma,eBayes)
... ... 
@@ -74,8 +80,11 @@ importFrom(readxl,read_excel)
74 80 
 importFrom(scales,number_format)
75 81 
 importFrom(scater,runPCA)
76 82 
 importFrom(shiny,addResourcePath)
83 
+importFrom(shiny,column)
84 
+importFrom(shiny,downloadButton)
77 85 
 importFrom(shiny,downloadHandler)
78 86 
 importFrom(shiny,eventReactive)
87 
+importFrom(shiny,fluidRow)
79 88 
 importFrom(shiny,icon)
80 89 
 importFrom(shiny,observeEvent)
81 90 
 importFrom(shiny,radioButtons)
... ... 
@@ -100,8 +109,8 @@ importFrom(standR,findNCGs)
100 109 
 importFrom(standR,geomxBatchCorrection)
101 110 
 importFrom(standR,geomxNorm)
102 111 
 importFrom(standR,readGeoMx)
103 
-importFrom(stats,filter)
104 112 
 importFrom(stats,model.matrix)
113 
+importFrom(tibble,num)
105 114 
 importFrom(tibble,rownames_to_column)
106 115 
 importFrom(utils,combn)
107 116 
 importFrom(utils,de)
Browse code

Added a new setup nav panel. Moved sidebar UI. Handled file upload edge cases. Enabled more show/hide nav panel logic.

kimsjune authored on 18/10/2024 20:01:53
Showing 1 changed files
NAMESPACE
History View file @ 25ed8ff
... ... 
@@ -19,7 +19,9 @@ importFrom(bslib,accordion)
19 19 
 importFrom(bslib,accordion_panel)
20 20 
 importFrom(bslib,layout_columns)
21 21 
 importFrom(bslib,layout_sidebar)
22 
+importFrom(bslib,nav_hide)
22 23 
 importFrom(bslib,nav_panel)
24 
+importFrom(bslib,nav_show)
23 25 
 importFrom(bslib,page_fillable)
24 26 
 importFrom(bslib,page_navbar)
25 27 
 importFrom(bslib,sidebar)
... ... 
@@ -50,6 +52,8 @@ importFrom(ggplot2,xlab)
50 52 
 importFrom(ggplot2,xlim)
51 53 
 importFrom(ggplot2,ylab)
52 54 
 importFrom(ggplot2,ylim)
55 
+importFrom(ggpubr,as_ggplot)
56 
+importFrom(ggpubr,get_legend)
53 57 
 importFrom(ggrepel,geom_text_repel)
54 58 
 importFrom(grDevices,dev.off)
55 59 
 importFrom(grDevices,png)
Browse code

Implemented heatmap. Column labels and split by group not working yet.

kimsjune authored on 16/10/2024 20:21:37
Showing 1 changed files
NAMESPACE
History View file @ 6cccd06
... ... 
@@ -3,12 +3,16 @@
3 3 
 export(shinyDSP)
4 4 
 importFrom(AnnotationHub,query)
5 5 
 importFrom(BiocGenerics,as.list)
6 
+importFrom(ComplexHeatmap,Heatmap)
7 
+importFrom(ComplexHeatmap,HeatmapAnnotation)
8 
+importFrom(ComplexHeatmap,anno_block)
6 9 
 importFrom(DT,datatable)
7 10 
 importFrom(DT,formatSignif)
8 11 
 importFrom(DT,renderDT)
9 12 
 importFrom(ExperimentHub,ExperimentHub)
10 13 
 importFrom(S4Vectors,metadata)
11 14 
 importFrom(SingleCellExperiment,reducedDim)
15 
+importFrom(SummarizedExperiment,assay)
12 16 
 importFrom(SummarizedExperiment,colData)
13 17 
 importFrom(bsicons,bs_icon)
14 18 
 importFrom(bslib,accordion)
... ... 
@@ -19,10 +23,12 @@ importFrom(bslib,nav_panel)
19 23 
 importFrom(bslib,page_fillable)
20 24 
 importFrom(bslib,page_navbar)
21 25 
 importFrom(bslib,sidebar)
26 
+importFrom(circlize,colorRamp2)
22 27 
 importFrom(cowplot,plot_grid)
23 28 
 importFrom(cowplot,save_plot)
24 29 
 importFrom(dplyr,pull)
25 30 
 importFrom(dplyr,select)
31 
+importFrom(dplyr,slice_head)
26 32 
 importFrom(edgeR,SE2DGEList)
27 33 
 importFrom(edgeR,estimateDisp)
28 34 
 importFrom(edgeR,filterByExpr)
... ... 
@@ -47,6 +53,7 @@ importFrom(ggplot2,ylim)
47 53 
 importFrom(ggrepel,geom_text_repel)
48 54 
 importFrom(grDevices,dev.off)
49 55 
 importFrom(grDevices,png)
56 
+importFrom(grid,gpar)
50 57 
 importFrom(grid,unit)
51 58 
 importFrom(htmltools,div)
52 59 
 importFrom(limma,contrasts.fit)
Browse code

Working state save

kimsjune authored on 16/10/2024 03:32:02
Showing 1 changed files
NAMESPACE
History View file @ 861d6d6
... ... 
@@ -52,6 +52,7 @@ importFrom(htmltools,div)
52 52 
 importFrom(limma,contrasts.fit)
53 53 
 importFrom(limma,duplicateCorrelation)
54 54 
 importFrom(limma,eBayes)
55 
+importFrom(limma,is.fullrank)
55 56 
 importFrom(limma,lmFit)
56 57 
 importFrom(limma,makeContrasts)
57 58 
 importFrom(limma,topTable)
Browse code

Implementing ExperimentHub demo data. Added custom experimental variable selection.

kimsjune authored on 12/10/2024 07:13:48
Showing 1 changed files
NAMESPACE
History View file @ d2cbae3
... ... 
@@ -1,10 +1,12 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export(ShinyDSP)
3 
+export(shinyDSP)
4 
+importFrom(AnnotationHub,query)
4 5 
 importFrom(BiocGenerics,as.list)
5 6 
 importFrom(DT,datatable)
6 7 
 importFrom(DT,formatSignif)
7 8 
 importFrom(DT,renderDT)
9 
+importFrom(ExperimentHub,ExperimentHub)
8 10 
 importFrom(S4Vectors,metadata)
9 11 
 importFrom(SingleCellExperiment,reducedDim)
10 12 
 importFrom(SummarizedExperiment,colData)
... ... 
@@ -55,6 +57,7 @@ importFrom(limma,makeContrasts)
55 57 
 importFrom(limma,topTable)
56 58 
 importFrom(limma,voom)
57 59 
 importFrom(magrittr,"%>%")
60 
+importFrom(readr,read_delim)
58 61 
 importFrom(readxl,read_excel)
59 62 
 importFrom(scales,number_format)
60 63 
 importFrom(scater,runPCA)
... ... 
@@ -69,6 +72,7 @@ importFrom(shiny,renderDataTable)
69 72 
 importFrom(shiny,renderPlot)
70 73 
 importFrom(shiny,renderText)
71 74 
 importFrom(shiny,renderUI)
75 
+importFrom(shiny,runApp)
72 76 
 importFrom(shiny,selectInput)
73 77 
 importFrom(shiny,sliderInput)
74 78 
 importFrom(shiny,tags)
Browse code

Added a README and testthat

kimsjune authored on 10/10/2024 04:43:28
Showing 1 changed files
NAMESPACE
History View file @ 7735e6b
... ... 
@@ -1,11 +1,11 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export(build_app)
3 
+export(ShinyDSP)
4 4 
 importFrom(BiocGenerics,as.list)
5 
-importFrom(DT,"%>%")
6 5 
 importFrom(DT,datatable)
7 6 
 importFrom(DT,formatSignif)
8 7 
 importFrom(DT,renderDT)
8 
+importFrom(S4Vectors,metadata)
9 9 
 importFrom(SingleCellExperiment,reducedDim)
10 10 
 importFrom(SummarizedExperiment,colData)
11 11 
 importFrom(bsicons,bs_icon)
... ... 
@@ -24,7 +24,6 @@ importFrom(dplyr,select)
24 24 
 importFrom(edgeR,SE2DGEList)
25 25 
 importFrom(edgeR,estimateDisp)
26 26 
 importFrom(edgeR,filterByExpr)
27 
-importFrom(fontawesome,fa)
28 27 
 importFrom(ggplot2,aes)
29 28 
 importFrom(ggplot2,geom_hline)
30 29 
 importFrom(ggplot2,geom_point)
... ... 
@@ -40,13 +39,14 @@ importFrom(ggplot2,scale_y_continuous)
40 39 
 importFrom(ggplot2,theme)
41 40 
 importFrom(ggplot2,theme_bw)
42 41 
 importFrom(ggplot2,xlab)
42 
+importFrom(ggplot2,xlim)
43 43 
 importFrom(ggplot2,ylab)
44 
+importFrom(ggplot2,ylim)
44 45 
 importFrom(ggrepel,geom_text_repel)
45 46 
 importFrom(grDevices,dev.off)
46 47 
 importFrom(grDevices,png)
47 48 
 importFrom(grid,unit)
48 49 
 importFrom(htmltools,div)
49 
-importFrom(htmltools,tags)
50 50 
 importFrom(limma,contrasts.fit)
51 51 
 importFrom(limma,duplicateCorrelation)
52 52 
 importFrom(limma,eBayes)
... ... 
@@ -54,6 +54,7 @@ importFrom(limma,lmFit)
54 54 
 importFrom(limma,makeContrasts)
55 55 
 importFrom(limma,topTable)
56 56 
 importFrom(limma,voom)
57 
+importFrom(magrittr,"%>%")
57 58 
 importFrom(readxl,read_excel)
58 59 
 importFrom(scales,number_format)
59 60 
 importFrom(scater,runPCA)
... ... 
@@ -86,6 +87,7 @@ importFrom(standR,readGeoMx)
86 87 
 importFrom(stats,filter)
87 88 
 importFrom(stats,model.matrix)
88 89 
 importFrom(tibble,rownames_to_column)
90 
+importFrom(utils,combn)
89 91 
 importFrom(utils,de)
90 92 
 importFrom(utils,write.table)
91 93 
 importFrom(withr,with_options)
Browse code

Initial

kimsjune authored on 09/10/2024 21:14:47
Showing 1 changed files
NAMESPACE
History View file @ 1b2b1da
... ... 
@@ -1,2 +1,91 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(build_app)
4 
+importFrom(BiocGenerics,as.list)
5 
+importFrom(DT,"%>%")
6 
+importFrom(DT,datatable)
7 
+importFrom(DT,formatSignif)
8 
+importFrom(DT,renderDT)
9 
+importFrom(SingleCellExperiment,reducedDim)
10 
+importFrom(SummarizedExperiment,colData)
11 
+importFrom(bsicons,bs_icon)
12 
+importFrom(bslib,accordion)
13 
+importFrom(bslib,accordion_panel)
14 
+importFrom(bslib,layout_columns)
15 
+importFrom(bslib,layout_sidebar)
16 
+importFrom(bslib,nav_panel)
17 
+importFrom(bslib,page_fillable)
18 
+importFrom(bslib,page_navbar)
19 
+importFrom(bslib,sidebar)
20 
+importFrom(cowplot,plot_grid)
21 
+importFrom(cowplot,save_plot)
22 
+importFrom(dplyr,pull)
23 
+importFrom(dplyr,select)
24 
+importFrom(edgeR,SE2DGEList)
25 
+importFrom(edgeR,estimateDisp)
26 
+importFrom(edgeR,filterByExpr)
27 
+importFrom(fontawesome,fa)
28 
+importFrom(ggplot2,aes)
29 
+importFrom(ggplot2,geom_hline)
30 
+importFrom(ggplot2,geom_point)
31 
+importFrom(ggplot2,geom_vline)
32 
+importFrom(ggplot2,ggtitle)
33 
+importFrom(ggplot2,guides)
34 
+importFrom(ggplot2,labs)
35 
+importFrom(ggplot2,scale_colour_manual)
36 
+importFrom(ggplot2,scale_fill_manual)
37 
+importFrom(ggplot2,scale_shape_manual)
38 
+importFrom(ggplot2,scale_x_continuous)
39 
+importFrom(ggplot2,scale_y_continuous)
40 
+importFrom(ggplot2,theme)
41 
+importFrom(ggplot2,theme_bw)
42 
+importFrom(ggplot2,xlab)
43 
+importFrom(ggplot2,ylab)
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+importFrom(ggrepel,geom_text_repel)
45 
+importFrom(grDevices,dev.off)
46 
+importFrom(grDevices,png)
47 
+importFrom(grid,unit)
48 
+importFrom(htmltools,div)
49 
+importFrom(htmltools,tags)
50 
+importFrom(limma,contrasts.fit)
51 
+importFrom(limma,duplicateCorrelation)
52 
+importFrom(limma,eBayes)
53 
+importFrom(limma,lmFit)
54 
+importFrom(limma,makeContrasts)
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+importFrom(limma,topTable)
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+importFrom(limma,voom)
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+importFrom(readxl,read_excel)
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+importFrom(scales,number_format)
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+importFrom(scater,runPCA)
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+importFrom(shiny,addResourcePath)
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+importFrom(shiny,downloadHandler)
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+importFrom(shiny,eventReactive)
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+importFrom(shiny,icon)
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+importFrom(shiny,observeEvent)
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+importFrom(shiny,radioButtons)
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+importFrom(shiny,reactive)
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+importFrom(shiny,renderDataTable)
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+importFrom(shiny,renderPlot)
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+importFrom(shiny,renderText)
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+importFrom(shiny,renderUI)
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+importFrom(shiny,selectInput)
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+importFrom(shiny,sliderInput)
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+importFrom(shiny,tags)
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+importFrom(shiny,uiOutput)
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+importFrom(shinyWidgets,radioGroupButtons)
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+importFrom(shinycssloaders,withSpinner)
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+importFrom(shinyjs,hidden)
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+importFrom(shinyjs,hide)
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+importFrom(shinyjs,show)
80 
+importFrom(shinyjs,toggle)
81 
+importFrom(shinyjs,useShinyjs)
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+importFrom(standR,findNCGs)
83 
+importFrom(standR,geomxBatchCorrection)
84 
+importFrom(standR,geomxNorm)
85 
+importFrom(standR,readGeoMx)
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+importFrom(stats,filter)
87 
+importFrom(stats,model.matrix)
88 
+importFrom(tibble,rownames_to_column)
89 
+importFrom(utils,de)
90 
+importFrom(utils,write.table)
91 
+importFrom(withr,with_options)
Browse code

Initial commit

kimsjune authored on 04/10/2024 16:46:08
Showing 1 changed files
NAMESPACE
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+# Generated by roxygen2: do not edit by hand
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