_Sidebar.md
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@@ -5,9 +5,11 @@ Installing Software
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* [Supported Operating Systems](operatingsystems)
6 6
* [Installation: 'Site' installation](installation_admin)
7 7
* [Installation: MacOS GUI](client_install)
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-* [Installation: Package Manager](client_CLI_install)
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+* [Installation: CLI Installer](client_CLI_install)
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+* [Available Packages](https://biogrids.org/software/)
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+* [R Packages](r_packages)
9 11
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-Using the BIOGrids Environment
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+Using the BioGrids Environment
11 13
* [Getting Started with BioGrids](getting_started)
12 14
* [Overriding Software Versions](versions)
13 15
* [BioGrids environment: Capsules](capsules)
r_packages.md
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@@ -0,0 +1,282 @@
1
+## Available R Packages
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+
3
+R packages for the latest version of R are detailed in the table below.
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+
5
+
6
+| |Package Version |R Version |
7
+|:----------------------|:---------------|:---------|
8
+|acepack |1.4.1 |3.5.1 |
9
+|ade4 |1.7-13 |3.5.1 |
10
+|alakazam |0.2.11 |3.5.1 |
11
+|AneuFinderData |1.10.0 |3.5.1 |
12
+|AnnotationDbi |1.44.0 |3.5.1 |
13
+|AnnotationFilter |1.6.0 |3.5.1 |
14
+|AnnotationHub |2.14.5 |3.5.1 |
15
+|ape |5.3 |3.5.1 |
16
+|askpass |1.1 |3.5.1 |
17
+|assertive |0.3-5 |3.5.1 |
18
+|assertive.base |0.0-7 |3.5.1 |
19
+|assertive.code |0.0-3 |3.5.1 |
20
+|assertive.data |0.0-3 |3.5.1 |
21
+|assertive.data.uk |0.0-2 |3.5.1 |
22
+|assertive.data.us |0.0-2 |3.5.1 |
23
+|assertive.datetimes |0.0-2 |3.5.1 |
24
+|assertive.files |0.0-2 |3.5.1 |
25
+|assertive.matrices |0.0-2 |3.5.1 |
26
+|assertive.models |0.0-2 |3.5.1 |
27
+|assertive.numbers |0.0-2 |3.5.1 |
28
+|assertive.properties |0.0-4 |3.5.1 |
29
+|assertive.reflection |0.0-4 |3.5.1 |
30
+|assertive.sets |0.0-3 |3.5.1 |
31
+|assertive.strings |0.0-3 |3.5.1 |
32
+|assertive.types |0.0-3 |3.5.1 |
33
+|assertthat |0.2.1 |3.5.1 |
34
+|backports |1.1.4 |3.5.1 |
35
+|base64enc |0.1-3 |3.5.1 |
36
+|basejump |0.7.2 |3.5.1 |
37
+|bcbioBase |0.4.1 |3.5.1 |
38
+|bcbioSingleCell |0.2.1 |3.5.1 |
39
+|BH |1.69.0-1 |3.5.1 |
40
+|bibtex |0.4.2 |3.5.1 |
41
+|Biobase |2.42.0 |3.5.1 |
42
+|BiocGenerics |0.28.0 |3.5.1 |
43
+|BiocManager |1.30.4 |3.5.1 |
44
+|BiocParallel |1.16.6 |3.5.1 |
45
+|BiocVersion |3.8.0 |3.5.1 |
46
+|biomaRt |2.38.0 |3.5.1 |
47
+|Biostrings |2.50.2 |3.5.1 |
48
+|bit |1.1-14 |3.5.1 |
49
+|bit64 |0.9-7 |3.5.1 |
50
+|bitops |1.0-6 |3.5.1 |
51
+|blob |1.1.1 |3.5.1 |
52
+|broom |0.5.2 |3.5.1 |
53
+|callr |3.2.0 |3.5.1 |
54
+|caTools |1.17.1.2 |3.5.1 |
55
+|cellranger |1.1.0 |3.5.1 |
56
+|checkmate |1.9.1 |3.5.1 |
57
+|cli |1.1.0 |3.5.1 |
58
+|clipr |0.6.0 |3.5.1 |
59
+|colorspace |1.4-1 |3.5.1 |
60
+|cowplot |0.9.4 |3.5.1 |
61
+|crayon |1.3.4 |3.5.1 |
62
+|crosstalk |1.0.0 |3.5.1 |
63
+|curl |3.3 |3.5.1 |
64
+|data.table |1.12.2 |3.5.1 |
65
+|DBI |1.0.0 |3.5.1 |
66
+|dbplyr |1.3.0 |3.5.1 |
67
+|DelayedArray |0.8.0 |3.5.1 |
68
+|dendsort |0.3.3 |3.5.1 |
69
+|DEoptimR |1.0-8 |3.5.1 |
70
+|digest |0.6.18 |3.5.1 |
71
+|diptest |0.75-7 |3.5.1 |
72
+|DNAcopy |1.56.0 |3.5.1 |
73
+|doParallel |1.0.14 |3.5.1 |
74
+|doSNOW |1.0.16 |3.5.1 |
75
+|dplyr |0.8.0.1 |3.5.1 |
76
+|dtw |1.20-1 |3.5.1 |
77
+|ecp |3.1.1 |3.5.1 |
78
+|ellipsis |0.1.0 |3.5.1 |
79
+|ensembldb |2.6.8 |3.5.1 |
80
+|evaluate |0.13 |3.5.1 |
81
+|fansi |0.4.0 |3.5.1 |
82
+|fitdistrplus |1.0-14 |3.5.1 |
83
+|flexmix |2.3-15 |3.5.1 |
84
+|forcats |0.4.0 |3.5.1 |
85
+|foreach |1.4.4 |3.5.1 |
86
+|formatR |1.6 |3.5.1 |
87
+|Formula |1.2-3 |3.5.1 |
88
+|fpc |2.1-11.1 |3.5.1 |
89
+|fs |1.2.7 |3.5.1 |
90
+|futile.logger |1.4.3 |3.5.1 |
91
+|futile.options |1.0.1 |3.5.1 |
92
+|future |1.12.0 |3.5.1 |
93
+|future.apply |1.2.0 |3.5.1 |
94
+|gbRd |0.4-11 |3.5.1 |
95
+|gdata |2.18.0 |3.5.1 |
96
+|generics |0.0.2 |3.5.1 |
97
+|GenomeInfoDb |1.18.2 |3.5.1 |
98
+|GenomeInfoDbData |1.2.0 |3.5.1 |
99
+|GenomicAlignments |1.18.1 |3.5.1 |
100
+|GenomicFeatures |1.34.8 |3.5.1 |
101
+|GenomicRanges |1.34.0 |3.5.1 |
102
+|GGally |1.4.0 |3.5.1 |
103
+|ggdendro |0.1-20 |3.5.1 |
104
+|ggplot2 |3.1.1 |3.5.1 |
105
+|ggrepel |0.8.0 |3.5.1 |
106
+|ggridges |0.5.1 |3.5.1 |
107
+|globals |0.12.4 |3.5.1 |
108
+|glue |1.3.1 |3.5.1 |
109
+|gplots |3.0.1.1 |3.5.1 |
110
+|gridExtra |2.3 |3.5.1 |
111
+|grr |0.9.5 |3.5.1 |
112
+|gtable |0.3.0 |3.5.1 |
113
+|gtools |3.8.1 |3.5.1 |
114
+|haven |2.1.0 |3.5.1 |
115
+|hdf5r |1.1.1 |3.5.1 |
116
+|hexbin |1.27.2 |3.5.1 |
117
+|highr |0.8 |3.5.1 |
118
+|Hmisc |4.2-0 |3.5.1 |
119
+|hms |0.4.2 |3.5.1 |
120
+|htmlTable |1.13.1 |3.5.1 |
121
+|htmltools |0.3.6 |3.5.1 |
122
+|htmlwidgets |1.3 |3.5.1 |
123
+|httpuv |1.5.1 |3.5.1 |
124
+|httr |1.4.0 |3.5.1 |
125
+|ica |1.0-2 |3.5.1 |
126
+|igraph |1.2.4 |3.5.1 |
127
+|interactiveDisplayBase |1.20.0 |3.5.1 |
128
+|IRanges |2.16.0 |3.5.1 |
129
+|irlba |2.3.3 |3.5.1 |
130
+|iterators |1.0.10 |3.5.1 |
131
+|jsonlite |1.6 |3.5.1 |
132
+|kedd |1.0.3 |3.5.1 |
133
+|kernlab |0.9-27 |3.5.1 |
134
+|knitr |1.22 |3.5.1 |
135
+|labeling |0.3 |3.5.1 |
136
+|lambda.r |1.2.3 |3.5.1 |
137
+|lars |1.2 |3.5.1 |
138
+|later |0.8.0 |3.5.1 |
139
+|latticeExtra |0.6-28 |3.5.1 |
140
+|lazyeval |0.2.2 |3.5.1 |
141
+|listenv |0.7.0 |3.5.1 |
142
+|lmtest |0.9-36 |3.5.1 |
143
+|lsei |1.2-0 |3.5.1 |
144
+|lubridate |1.7.4 |3.5.1 |
145
+|magrittr |1.5 |3.5.1 |
146
+|markdown |0.9 |3.5.1 |
147
+|Matrix.utils |0.9.7 |3.5.1 |
148
+|matrixStats |0.54.0 |3.5.1 |
149
+|mclust |5.4.3 |3.5.1 |
150
+|memoise |1.1.0 |3.5.1 |
151
+|metap |1.1 |3.5.1 |
152
+|mime |0.6 |3.5.1 |
153
+|mixtools |1.1.0 |3.5.1 |
154
+|modelr |0.1.4 |3.5.1 |
155
+|modeltools |0.2-22 |3.5.1 |
156
+|munsell |0.5.0 |3.5.1 |
157
+|mvtnorm |1.0-10 |3.5.1 |
158
+|npsurv |0.4-0 |3.5.1 |
159
+|openssl |1.3 |3.5.1 |
160
+|openxlsx |4.1.0 |3.5.1 |
161
+|pbapply |1.4-0 |3.5.1 |
162
+|pheatmap |1.0.12 |3.5.1 |
163
+|pillar |1.3.1 |3.5.1 |
164
+|pkgconfig |2.0.2 |3.5.1 |
165
+|plogr |0.2.0 |3.5.1 |
166
+|plotly |4.9.0 |3.5.1 |
167
+|plyr |1.8.4 |3.5.1 |
168
+|png |0.1-7 |3.5.1 |
169
+|prabclus |2.2-7 |3.5.1 |
170
+|prettyunits |1.0.2 |3.5.1 |
171
+|processx |3.3.0 |3.5.1 |
172
+|progress |1.2.0 |3.5.1 |
173
+|promises |1.0.1 |3.5.1 |
174
+|ProtGenerics |1.14.0 |3.5.1 |
175
+|proxy |0.4-23 |3.5.1 |
176
+|ps |1.3.0 |3.5.1 |
177
+|purrr |0.3.2 |3.5.1 |
178
+|R.methodsS3 |1.7.1 |3.5.1 |
179
+|R.oo |1.22.0 |3.5.1 |
180
+|R.utils |2.8.0 |3.5.1 |
181
+|R6 |2.4.0 |3.5.1 |
182
+|RANN |2.6.1 |3.5.1 |
183
+|RColorBrewer |1.1-2 |3.5.1 |
184
+|Rcpp |1.0.1 |3.5.1 |
185
+|RcppEigen |0.3.3.5.0 |3.5.1 |
186
+|RcppProgress |0.4.1 |3.5.1 |
187
+|RCurl |1.95-4.12 |3.5.1 |
188
+|Rdpack |0.11-0 |3.5.1 |
189
+|rdrop2 |0.8.1 |3.5.1 |
190
+|readr |1.3.1 |3.5.1 |
191
+|readxl |1.3.1 |3.5.1 |
192
+|rematch |1.0.1 |3.5.1 |
193
+|remotes |2.0.4 |3.5.1 |
194
+|ReorderCluster |1.0 |3.5.1 |
195
+|reprex |0.2.1 |3.5.1 |
196
+|reshape |0.8.8 |3.5.1 |
197
+|reshape2 |1.4.3 |3.5.1 |
198
+|reticulate |1.12 |3.5.1 |
199
+|rhdf5 |2.26.2 |3.5.1 |
200
+|rio |0.5.16 |3.5.1 |
201
+|rlang |0.3.4 |3.5.1 |
202
+|rmarkdown |1.12 |3.5.1 |
203
+|robustbase |0.93-4 |3.5.1 |
204
+|ROCR |1.0-7 |3.5.1 |
205
+|Rsamtools |1.34.1 |3.5.1 |
206
+|RSQLite |2.1.1 |3.5.1 |
207
+|rstudioapi |0.10 |3.5.1 |
208
+|rsvd |1.0.0 |3.5.1 |
209
+|rtracklayer |1.42.2 |3.5.1 |
210
+|Rtsne |0.15 |3.5.1 |
211
+|rvest |0.3.3 |3.5.1 |
212
+|S4Vectors |0.20.1 |3.5.1 |
213
+|scales |1.0.0 |3.5.1 |
214
+|scrm |1.7.3-1 |3.5.1 |
215
+|sctransform |0.2.0 |3.5.1 |
216
+|SDMTools |1.1-221 |3.5.1 |
217
+|segmented |0.5-3.0 |3.5.1 |
218
+|selectr |0.4-1 |3.5.1 |
219
+|seqinr |3.4-5 |3.5.1 |
220
+|sessioninfo |1.1.1 |3.5.1 |
221
+|Seurat |3.0.0 |3.5.1 |
222
+|shazam |0.1.11 |3.5.1 |
223
+|shiny |1.3.1 |3.5.1 |
224
+|SingleCellExperiment |1.4.1 |3.5.1 |
225
+|snow |0.4-3 |3.5.1 |
226
+|sourcetools |0.1.7 |3.5.1 |
227
+|stringi |1.4.3 |3.5.1 |
228
+|stringr |1.4.0 |3.5.1 |
229
+|SummarizedExperiment |1.12.0 |3.5.1 |
230
+|sys |3.1 |3.5.1 |
231
+|tibble |2.1.1 |3.5.1 |
232
+|tidyr |0.8.3 |3.5.1 |
233
+|tidyselect |0.2.5 |3.5.1 |
234
+|tidyverse |1.2.1 |3.5.1 |
235
+|tigger |0.3.1 |3.5.1 |
236
+|tinytex |0.12 |3.5.1 |
237
+|trimcluster |0.1-2.1 |3.5.1 |
238
+|tsne |0.1-3 |3.5.1 |
239
+|utf8 |1.1.4 |3.5.1 |
240
+|viridis |0.5.1 |3.5.1 |
241
+|viridisLite |0.3.0 |3.5.1 |
242
+|whisker |0.3-2 |3.5.1 |
243
+|withr |2.1.2 |3.5.1 |
244
+|xfun |0.6 |3.5.1 |
245
+|XML |3.98-1.19 |3.5.1 |
246
+|xml2 |1.2.0 |3.5.1 |
247
+|xtable |1.8-3 |3.5.1 |
248
+|XVector |0.22.0 |3.5.1 |
249
+|yaml |2.2.0 |3.5.1 |
250
+|zip |2.0.1 |3.5.1 |
251
+|zlibbioc |1.28.0 |3.5.1 |
252
+|zoo |1.8-5 |3.5.1 |
253
+|base |3.5.1 |3.5.1 |
254
+|boot |1.3-20 |3.5.1 |
255
+|class |7.3-15 |3.5.1 |
256
+|cluster |2.0.8 |3.5.1 |
257
+|codetools |0.2-16 |3.5.1 |
258
+|compiler |3.5.1 |3.5.1 |
259
+|datasets |3.5.1 |3.5.1 |
260
+|foreign |0.8-71 |3.5.1 |
261
+|graphics |3.5.1 |3.5.1 |
262
+|grDevices |3.5.1 |3.5.1 |
263
+|grid |3.5.1 |3.5.1 |
264
+|KernSmooth |2.23-15 |3.5.1 |
265
+|lattice |0.20-38 |3.5.1 |
266
+|MASS |7.3-51.3 |3.5.1 |
267
+|Matrix |1.2-17 |3.5.1 |
268
+|methods |3.5.1 |3.5.1 |
269
+|mgcv |1.8-28 |3.5.1 |
270
+|nlme |3.1-139 |3.5.1 |
271
+|nnet |7.3-12 |3.5.1 |
272
+|parallel |3.5.1 |3.5.1 |
273
+|Rhdf5lib |1.4.3 |3.5.1 |
274
+|rpart |4.1-15 |3.5.1 |
275
+|spatial |7.3-11 |3.5.1 |
276
+|splines |3.5.1 |3.5.1 |
277
+|stats |3.5.1 |3.5.1 |
278
+|stats4 |3.5.1 |3.5.1 |
279
+|survival |2.44-1.1 |3.5.1 |
280
+|tcltk |3.5.1 |3.5.1 |
281
+|tools |3.5.1 |3.5.1 |
282
+|utils |3.5.1 |3.5.1 |