73ea220301252e9813dd132557dc241a59b9c618
_Sidebar.md
... | ... | @@ -5,9 +5,11 @@ Installing Software |
5 | 5 | * [Supported Operating Systems](operatingsystems) |
6 | 6 | * [Installation: 'Site' installation](installation_admin) |
7 | 7 | * [Installation: MacOS GUI](client_install) |
8 | -* [Installation: Package Manager](client_CLI_install) |
|
8 | +* [Installation: CLI Installer](client_CLI_install) |
|
9 | +* [Available Packages](https://biogrids.org/software/) |
|
10 | +* [R Packages](r_packages) |
|
9 | 11 | |
10 | -Using the BIOGrids Environment |
|
12 | +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
... | ... | @@ -0,0 +1,282 @@ |
1 | +## Available R Packages |
|
2 | + |
|
3 | +R packages for the latest version of R are detailed in the table below. |
|
4 | + |
|
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 | |