LoadPackages.R 3.75 KB
Newer Older
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
1
2
options(download.file.method = 'wget')

svolant's avatar
svolant committed
3

svolant's avatar
svolant committed
4
if (!require("shinytoastr")){
5
  devtools::install_github("mangothecat/shinytoastr")
svolant's avatar
svolant committed
6
7
8
9
  library(shinytoastr)
}

if (!require("shinyWidgets")){
10
  devtools::install_github("aghozlane/shinyWidgets")
svolant's avatar
svolant committed
11
12
13
14
15
  library(shinyWidgets)
}



svolant's avatar
svolant committed
16
17
18
19
20
if (!require("sendmailR")){
  install.packages("sendmailR")
  library(sendmailR)
}

svolant's avatar
svolant committed
21

svolant's avatar
svolant committed
22
23
24
25
26
27
28
29
30
31
if (!require("shinyBS")){
  install.packages("shinyBS")
  library(shinyBS)
}

library(tools)

if (!require("flexdashboard")){
  install.packages("flexdashboard")
  library(flexdashboard)
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
32
}
svolant's avatar
svolant committed
33

svolant's avatar
svolant committed
34
35
if (!require("backports")){
  install.packages("backports")
svolant's avatar
svolant committed
36
  library(backports)
svolant's avatar
svolant committed
37
38
}

svolant's avatar
svolant committed
39

svolant's avatar
svolant committed
40
41
if (!require("readr")){
  install.packages("readr")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
42
  library(readr)
svolant's avatar
svolant committed
43
44
45
46
}

if (!require("jsonlite")){
  install.packages("jsonlite")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
47
  library(jsonlite)
svolant's avatar
svolant committed
48
49
50
51
52
}


if (!require("shinyFiles")){
  install.packages("shinyFiles")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
53
  library(shinyFiles)
svolant's avatar
svolant committed
54
55
56
}


svolant's avatar
svolant committed
57
58
59
if (!require("Rcpp")){
  install.packages("Rcpp")
}
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
60
61
62
63
if(!require(shiny)){
  install.packages("shiny")
  library(shiny)
}
svolant's avatar
svolant committed
64
if(!require(shinydashboard)){
svolant's avatar
svolant committed
65
  devtools::install_github('aghozlane/shinydashboard')
svolant's avatar
svolant committed
66
67
68
69
70
  library(shinydashboard)
}

if(!require(rjson)){
  install.packages('rjson')
svolant's avatar
svolant committed
71
72
73
74
75
76
77
78
79
80
  library(rjson)
}
if(!require(ape)){
  install.packages('ape')
  library(ape)
}

if(!require(GUniFrac)){
  install.packages('GUniFrac')
  library(GUniFrac)
svolant's avatar
svolant committed
81
82
83
84
}

if(!require(devtools)){
  install.packages('devtools')
svolant's avatar
svolant committed
85
  library(devtools)
svolant's avatar
svolant committed
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
115
116
117
}

if (!require(psych)) {
  install.packages('psych')
  library(psych)
}

if (!require(ggplot2)) {
  install.packages('ggplot2')
  library(ggplot2)
}

if (!require(vegan)) {
  install.packages('vegan')
  library(vegan)
}

if (!require(dendextend)) {
  install.packages('dendextend')
  library(dendextend)
}

if (!require(circlize)) {
  install.packages('circlize')
  library(circlize)
}


if (!require(devtools)) {
  install.packages('devtools')
  library(devtools)
}
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
118
119
120
121
if(!require(treeWeightD3)){
   devtools::install_github('pierreLec/treeWeightD3')
   library(treeWeightD3)
}
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
122
123
124
125
126
if (!require(BiocInstaller)){
  source("https://bioconductor.org/biocLite.R")
  biocLite("BiocInstaller")
  library(BiocInstaller)
}
svolant's avatar
svolant committed
127

128
129
130
131
132
if (!require(d3heatmap)) {
  devtools::install_github('aghozlane/d3heatmap')
  library(d3heatmap)
}

133
134
# Let us use biomformat instead of biom
if (!require(biomformat)){
135
 devtools::install_github("aghozlane/biomformat")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
136
library(biomformat)
137
138
}

svolant's avatar
svolant committed
139
if (!require(scatterD3)) {
140
  devtools::install_github('aghozlane/scatterD3')
svolant's avatar
svolant committed
141
142
143
144
  library(scatterD3)
}

if (!require(rNVD3)) {
145
  devtools::install_github('aghozlane/rNVD3')
svolant's avatar
svolant committed
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
  library(rNVD3)
}

if (!require(genefilter)) {
  source("https://bioconductor.org/biocLite.R")
  biocLite("genefilter")
  library(genefilter)
}

if (!require(googleVis)) {
  install.packages('googleVis')
  suppressPackageStartupMessages(library(googleVis))
}

if (!require(shinyjs)) {
  install.packages('shinyjs')
  library(shinyjs)
}

if(!require(d3vennR)){
  install_github("timelyportfolio/d3vennR")
  library(d3vennR)
}

if (!require(DT)) {
  install.packages('DT')
  library(DT)
}

if (!require(RColorBrewer)) {
  install.packages('RColorBrewer')
  library(RColorBrewer)
}

if (!require(gplots)) {
  install.packages('gplots')
  library(gplots)
}

if (!require(DESeq2)) {
  source("https://bioconductor.org/biocLite.R")
  biocLite("DESeq2")
  library(DESeq2)
}

if (!require(ade4)) {
  install.packages('ade4')
  library(ade4)
}

if (!require(scales)) {
  install.packages('scales')
  library(scales)
}
svolant's avatar
svolant committed
200
201
202
203
204
205

if (!require(phytools)) {
  install.packages('phytools')
  library(phytools)
}

206
207
208
209
if(!require(philentropy)){
  devtools::install_github("HajkD/philentropy", build_vignettes = TRUE, dependencies = TRUE)
  library(philentropy)
}
svolant's avatar
svolant committed
210

211
if(!require(PhyloTreeMetaR)){
212
  devtools::install_github("pierreLec/PhyloTreeMetaR")
213
214
215
  library(PhyloTreeMetaR)
}

Amine  GHOZLANE's avatar
Amine GHOZLANE committed
216

217
218
219
220
# if(!require(plotly)){
#   install.packages("plotly")
#   library(plotly)  
# }
svolant's avatar
svolant committed
221
222