-
Notifications
You must be signed in to change notification settings - Fork 0
/
server-tab-About.R
114 lines (111 loc) · 6.48 KB
/
server-tab-About.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
#' =============================================================
#' @description ui output of About
#'==============================================================
output$About_ui <- renderUI({
fluidPage(
style = "background-color:#F0FFFF;",
HTML('<center><img src=\'./img/CMTCN_About.png\'
width="200" height="200"></center>'),
hr(),
column(
width = 2,
HTML('<p><p>
<a href="http://bioinforai.tech/wordpress/" target="_blank">
<img id="logo" alt="Lab Logo" src="./img/Logo_Lab.png" width="250"/>
</a>
<p><p>')
),
column(
width = 10,
HTML('
CMTCN was built using
<a href="http://shiny.rstudio.com/", target="_blank"> Shiny </a> by
<a href="https://www.rstudio.com/", target="_blank"> RStudio, </a> using open source software.<br><br>
We sincerely acknowledge all publicly available resources which have been used in CMTCN!<br><br>
The following R packages are utilized in no particular order of importance:<br>
<a href="http://shiny.rstudio.com/"> Shiny </a>(>=0.14.2)<br>
<a href="https://github.com/daattali/shinyjs">shinyjs</a>(>=0.8)<br>
<a href="http://rstudio.github.io/shinydashboard/">shinydashboard</a>(>=0.7.0)<br>
<a href="http://shiny.rstudio.com/articles/themes.html">shinythemes</a>(>=1.1.1)<br>
<a href="http://cran.r-project.org/web/packages/data.table/">data.table</a>(>=1.10.4-3)<br>
<a href="http://cran.r-project.org/package=DT">DT</a>(>=0.4)<br>
<a href="http://cran.r-project.org/web/packages/RSQLite/index.html">RSQLite</a>(>=2.1.0)<br>
<a href="https://cran.r-project.org/web/packages/DBI">DBI</a>(>=0.8)<br>
<a href="http://cran.r-project.org/web/packages/ggplot2/index.html">ggplot2</a>(>=2.2.1)<br>
<a href="http://cran.r-project.org/web/packages/ggthemes/index.html">ggthemes</a>(>=3.4.2)<br>
<a href="http://cran.r-project.org/package=networkD3">networkD3</a>(>=0.4)<br>
<a href="http://cran.r-project.org/package=dplyr">dplyr</a>(>=0.7.4)<br>
<a href="https://rmarkdown.rstudio.com/">markdown</a>(>=0.8)<br>
<a href="https://github.com/andrewsali/shinycssloaders">shinycssloaders</a>(>=0.2.0)<br>
<a href="http://www.bioconductor.org/packages/release/bioc/html/clusterProfiler.html">clusterProfiler</a>(>=3.8.0)<br>
<a href="http://www.bioconductor.org/packages/release/bioc/html/GSEABase.html">GSEABase</a>(>=1.42.0)<br>
<a href="http://cran.r-project.org/web/packages/igraph/index.html">igraph</a>(>=1.2.1)<br>
<a href="http://www.bioconductor.org/packages/release/bioc/html/RTCGAToolbox.html">RTCGAToolbox</a>(>=2.10.0)<br><br>
'),
HTML("TCGA expression data (run date 2016-01-28) provided in the <a href='http://gdac.broadinstitute.org/'>Firehose</a>
data repository are accessed using the R package RTCGAToolbox.<br><br>"),
HTML("A list of resources which are utilized in CMTCN"),
dataTableOutput("About_TBL")
# HTML(markdown::markdownToHTML())
)
)
})
output$About_TBL <- DT::renderDataTable({
Resource <- c(
'<a href="http://genomeportal.stanford.edu/pan-tcga/">TCGA-CE</a>',
'<a href="http://tcoa.cpu.edu.cn/index.php">The Cancer Omics Atlas</a>',
'<a href="http://gdac.broadinstitute.org/">Firehose</a>',
'<a href="http://itfp.biosino.org/itfp">ITFP</a>',
'<a href="www.grnpedia.org/trrust">TRRUST v2</a>',
'<a href="http://www.lbbc.ibb.unesp.br/htri">HTRIdb</a>',
'<a href="http://rulai.cshl.edu/TRED">TRED</a>',
'<a href="http://www.miR2Disease.org">miR2Disease</a>',
'<a href="http://miRTarBase.mbc.nctu.edu.tw/">miRTarBase</a>',
'<a href="http://c1.accurascience.com/miRecords/">miRecords</a>',
'<a href="http://starbase.sysu.edu.cn/">starBase</a>',
'<a href="http://www.targetscan.org/vert_70/">TargetScan</a>',
'<a href="http://mcube.nju.edu.cn/jwang/lab/soft/mirtrans/">mirTrans</a>',
'<a href="https://www.isical.ac.in/~bioinfo_miu/TF-miRNA1.php">PuTmiR</a>',
'<a href="https://www.intogen.org/search">IntOGen</a>',
'<a href="http://bioinfo.life.hust.edu.cn/SEGreg">SEGreg</a>',
'<a href="http://zhaobioinfo.org/TissGDB ">TissGDB</a>',
'<a href="http://www.cuilab.cn/hmdd">HMDD2.0</a>',
'<a href="http://mircancer.ecu.edu/">miRCancer</a>',
'<a href="http://www.miR2Disease.org">miR2Disease</a>',
'<a href="http://mips.helmholtz-muenchen.de/phenomir">PhenomiR</a>'
)
#Confidence <- c("Experimental","Experimental","Experimental","Predicted","Experimental","Experimental","Experimental","Predicted","Predicted","Experimental","Predicted")
Version <- c(
"V2.0",
"Aug.2018",
"Jan.2016",
"Aug.2008","V2.0","Aug.2012","Jan.2007","Apr.2008","V7.0","Apr.2013","V1.0","V7.0","Oct.2017","V1.1",
"Dec.2014","Jan.2018","Sep.2017",
"v2.0","Dec.2017","Apr.2008","Jan.2010"
)
Information <- c(
"Clinical-stage related genes",
"Top mutated genes",
"TCGA expression data",
"TF->Gene interactions","TF->Gene interactions","TF->Gene interactions","TF->Gene interactions",
"miRNA->Gene/TF interactions","miRNA->Gene/TF interactions","miRNA->Gene/TF interactions","miRNA->Gene/TF interactions","miRNA->Gene/TF interactions",
"TF->miRNA interactions","TF->miRNA interactions",
"Cancer gene information", "Cancer gene information", "Cancer gene information",
"Cancer miRNA information","Cancer miRNA information","Cancer miRNA information","Cancer miRNA information")
#nIter <- c(48861,8427,52467,7042,603,380639,1715,419578,100031,201364,10147)
CMTCN_Res <-
data.frame(
Resource,
# Confidence,
#nIter,
Version,
Information
)
colnames(CMTCN_Res) <- c("Resource","Version/Release.Date","Information")
DT::datatable(CMTCN_Res,
selection = "none",
filter = "none",
escape = 1,
options = list(pageLength = 10,dom = 'tip')
)
})