-
Notifications
You must be signed in to change notification settings - Fork 36
/
NEWS
448 lines (367 loc) · 17.1 KB
/
NEWS
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
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
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
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
CHANGES IN VERSION 3.5.2
------------------------
o bug fixed of gseaScores <2018-04-18, Wed>
+ https://github.com/GuangchuangYu/DOSE/issues/23
o mv web site to https://guangchuangyu.github.io/software/DOSE
CHANGES IN VERSION 3.3.2
------------------------
o new project site using blogdown <2017-09-28, Thu>
o ridgeplot for gseaResult <2017-08-17, Thu>
CHANGES IN VERSION 3.3.1
------------------------
o throw warning instead of error when fail to `setReadable`. <2017-06-28, Wed>
+ https://github.com/GuangchuangYu/clusterProfiler/issues/91
o better msg when using wrong ID types in GSEA <2017-06-01, Thu>
+ https://support.bioconductor.org/p/96512/#96516
CHANGES IN VERSION 3.2.0
------------------------
o BioC 3.5 release <2017-04-26, Wed>
CHANGES IN VERSION 3.1.3
------------------------
o output expected sample gene ID when input gene ID type not match <2017-03-27, Mon>
o dotplot for gseaResult <2016-11-23, Fri>
+ https://github.com/GuangchuangYu/DOSE/issues/20
CHANGES IN VERSION 3.1.2
------------------------
o in gseaplot, call grid.newpage only if dev.interactive() <2016-11-16, Wed>
o change minGSSize < geneSet_size & geneSet_size < maxGSSize to
minGSSize <= geneSet_size & geneSet_size <= maxGSSize <2016-11-16, Wed>
o fixed show method issus of unknown setType in clusterProfiler::GSEA output <2016-11-15, Tue>
o throw more friendly error msg if fail to determine setType automatically in setReadable function <2016-11-15, Tue>
+ https://support.bioconductor.org/p/89445/#89479
o apply minGSSize and maxGSSize to fgsea <2016-11-14, Mon>
o change summary to as.data.frame in internal calls to prevent warning message <2016-11-14, Mon>
CHANGES IN VERSION 3.1.1
------------------------
o update startup message <2016-11-09, Wed>
o fixed parallel in Windows (not supported) <2016-10-24, Mon>
+ https://github.com/GuangchuangYu/DOSE/issues/16
o options(DOSE_workers = x) to set using x cores for GSEA analysis is removed. <2016-10-24, Mon>
instead let MulticoreParam() to decide how many cores (can be set by `options(mc.cores = x)`).
CHANGES IN VERSION 3.0.0
------------------------
o BioC 3.4 released <2016-10-18, Tue>
CHANGES IN VERSION 2.11.12
------------------------
o deprecate summary method and use as.data.frame instead <2016-09-29, Thu>
CHANGES IN VERSION 2.11.11
------------------------
o export geneID and geneInCategory <2016-09-19, Mon>
CHANGES IN VERSION 2.11.10
------------------------
o geneID and geneInCategory accessor functions <2016-09-19, Mon>
CHANGES IN VERSION 2.11.9
------------------------
o enrichMap works with result contains only one term <2016-08-15, Wed>
+ https://github.com/GuangchuangYu/DOSE/issues/15
o build_Anno now works with tibble <2016-08-18, Tue>
CHANGES IN VERSION 2.11.8
------------------------
o add unit test <2016-08-15, Mon>
CHANGES IN VERSION 2.11.7
------------------------
o change for meshes packages <2016-08-11, Thu>
CHANGES IN VERSION 2.11.6
------------------------
o user can use options(DOSE_workers = x) to set using x cores for GSEA analysis <2016-08-02, Tue>
o support DisGeNET enrichment analyses <2016-08-01, Mon>
+ enrichDGN, enrichDGNv, gseDGN
o update vignettes <2016-07-29, Fri>
CHANGES IN VERSION 2.11.5
------------------------
o enrichMap now output igraph object that can be viewed using other software like networkD3 <2016-07-25, Mon>
o dim methods for enrichResult and gseaResult <2016-07-22, Fri>
o $ methods for enrichResult and gseaResult <2016-07-20, Wed>
o switch from parallel to BiocParallel <2017-07-07, Thu>
o [, head and tail methods for enrichResult and gseaResult <2016-07-06, Wed>
o change according to GOSemSim <2016-07-05, Tue>
CHANGES IN VERSION 2.11.4
------------------------
o 'title' parameter for gseaplot <2016-07-04, Mon>
+ contributed by https://github.com/pedrostrusso
+ https://github.com/GuangchuangYu/DOSE/pull/13
o 'by' parameter in GSEA_internal, by default by = 'fgsea' <2016-07-04, Mon>
+ by = 'fgsea', use GSEA algorithm implemented in fgsea
+ by = 'DOSE', use GSEA algorithm implemented in DOSE
o leading edge analysis for GSEA <2016-07-04, Mon>
CHANGES IN VERSION 2.11.3
------------------------
o output igraph object in cnetplot <2016-06-21, Tue>
o upsetplot generics <2016-06-14, Tue>
o [[ methods for enrichResult and gseaResult for accessing gene set <2016-06-14, Tue>
CHANGES IN VERSION 2.11.2
------------------------
o use byte compiler <2016-05-18, Wed>
o https://github.com/Bioconductor-mirror/DOSE/commit/6c508c6a6816f465bb372f30f4ab99c839d81767
CHANGES IN VERSION 2.11.1
------------------------
o https://github.com/Bioconductor-mirror/DOSE/commit/7e87d01e671ce1b5fbe974c06b796b1a2970f11c
CHANGES IN VERSION 2.10.0
------------------------
o BioC 3.3 released <2016-05-05, Thu>
CHANGES IN VERSION 2.9.7
------------------------
o barplot accepts x and colorBy parameters as in dotplot <2016-04-13, Wed>
o gsfilter function for restricting result with minimal and maximal gene set size <2016-03-31, Thu>
+ see https://github.com/GuangchuangYu/clusterProfiler/issues/46
CHANGES IN VERSION 2.9.6
------------------------
o add maxGSSize parameter for hypergeometric test <2016-03-09, Wed>
o add maxGSSize parameter in GSEA analysis. <2016-03-09, Wed>
+ Default of 500 is fairly standard for GSEA analysis.
+ Usually if the geneset > 500, its probability of being called significant by GSEA rises quite dramatically.
o fixed R check <2016-03-05, Sat>
o update ReactomePA citation info <2016-02-17, Wed>
CHANGES IN VERSION 2.9.5
------------------------
o upset plot for enrichResult object <2016-01-22, Fri>
CHANGES IN VERSION 2.9.4
------------------------
o bug fixed in scaling category sizes in enrichMap <2016-01-10, Sun>
+ use setSize in gseResult
CHANGES IN VERSION 2.9.3
------------------------
o update enrichMap to scale category sizes <2016-01-04, Mon>
o update 'show' methods of enrichResult and gseaResult <2015-12-29, Tue>
CHANGES IN VERSION 2.9.2
------------------------
o re-design internal function <2015-12-20, Sun>
CHANGES IN VERSION 2.9.1
------------------------
o GSEA: test bimodal separately <2015-10-28, Wed>
o add NES column in GSEA result <2015-10-28, Wed>
o use NES instead of ES in calculating p-values. <2015-10-28, Wed>
o duplicated gene IDs in enrich.internal is not allow. add `unique` to remove duplicated ID. <2015-10-20, Tue>
+ see https://github.com/GuangchuangYu/clusterProfiler/issues/27
CHANGES IN VERSION 2.9.0
------------------------
o BioC 3.3 branch
CHANGES IN VERSION 2.7.12
------------------------
o output a list of data frames by enrichMap via invisible, so that the graph info can be viewed by other tools, eg. Cytoscape. <2015-09-30, Wed>
CHANGES IN VERSION 2.7.11
------------------------
o check whether input geneList is sorted <2015-09-22, Tue>
o order first followed by showCategory subsetting in barplot <2015-09-08, Tue>
+ https://support.bioconductor.org/p/71917/#71939
o bug fixed in EXTID2NAME, keytype is TAIR for arabidopsis and ORF for malaria <2015-08-26, Wed>
CHANGES IN VERSION 2.7.10
------------------------
o add Giovanni Dall'Olio as contributor in author list. <2015-07-21, Tue>
o update NCG data to version cancergenes_4.9.0_20150720 contributed by Giovanni Dall'Olio.
https://github.com/GuangchuangYu/DOSE/pull/8 <2015-07-21, Tue>
o geneInCategory may simplify to vector by R in very rare case,
which violate the assumption of list in S4 validation checking.
This issue was fixed. <2015-07-19, Sun>
CHANGES IN VERSION 2.7.9
------------------------
o add citation of ChIPseeker <2015-07-09, Thu>
o add 'Disease analysis of NGS data' section in vignette <2015-06-29, Mon>
o convert vignette from Rnw to Rmd <2015-06-24, Wed>
CHANGES IN VERSION 2.7.8
------------------------
o dotplot for enrichResult <2015-06-21, Sun>
CHANGES IN VERSION 2.7.7
------------------------
o speed up by using sample.int instead of sample <2015-06-04, Thu>
o add seed = FALSE to control reproduciblility of gsea function.
to make result reproducible, explicitly set seed=TRUE <2015-06-04, Thu>
- contributed by Vlad, see https://github.com/GuangchuangYu/DOSE/pull/5/
- modified by Guangchuang
CHANGES IN VERSION 2.7.6
------------------------
o bug fixed in cnetplot legend contributed by Vladislav Petyuk <2015-05-28, Thu>
CHANGES IN VERSION 2.7.5
------------------------
o update vignette <2015-05-15, Fri>
CHANGES IN VERSION 2.7.4
------------------------
o update permutation test with pvalue = (K+1)/(N+1) instead of K/N,
so that p value will never be 0 <2015-05-12, Tue>
CHANGES IN VERSION 2.7.3
------------------------
o add setType slot in gseaResult <2015-05-15, Tue>
o add universe and geneSets slots in enrichResult <2015-05-05, Tue>
CHANGES IN VERSION 2.7.2
------------------------
o add vertex.label.font parameter in enrichMap <2015-04-27, Mon>
CHANGES IN VERSION 2.7.1
------------------------
o update NCG description in enrichNCG <2015-04-22, Wed>
CHANGES IN VERSION 2.5.12
------------------------
o report NA in qvalue column when it fail to calculate instead of throw error <2015-03-09, Thu>
o update IC data <2015-03-08, Wed>
CHANGES IN VERSION 2.5.11
------------------------
o implement clusterSim and mclusterSim <2015-03-07, Tue>
CHANGES IN VERSION 2.5.10
------------------------
o implement enrichNCG and now gseAnalyzer accept setType = "NCG" <2015-04-01, Wed>
see http://ncg.kcl.ac.uk
o change use_internal_data parameter to ... in all S3 generics and methods <2015-04-01, Wed>
CHANGES IN VERSION 2.5.9
------------------------
o extend gseAnalyzer to support use_internal_data parameter <2015-03-29, Sun>
CHANGES IN VERSION 2.5.8
------------------------
o keep order of barplot, sorted by pvalue by defalt <2015-02-11, Wed>
CHANGES IN VERSION 2.5.7
------------------------
o fixed typo in vignette <2015-02-10, Tue>
CHANGES IN VERSION 2.5.6
------------------------
o add organismMapper to satisfy the change of enrichKEGG <2015-01-28, Wed>
CHANGES IN VERSION 2.5.5
------------------------
o introduce use_internal_data parameter for enrichKEGG of clusterProfiler <2015-01-27, Tue>
CHANGES IN VERSION 2.5.3
------------------------
o update vignette <2015-01-27, Tue>
CHANGES IN VERSION 2.5.1
------------------------
o add CITATION <2015-01-19, Mon>
CHANGES IN VERSION 2.3.6
------------------------
o add readable parameter in simplot <2014-10-09, Thu>
CHANGES IN VERSION 2.3.5
------------------------
o implement enrichMap <2014-07-28, Wed>
CHANGES IN VERSION 2.3.4
------------------------
o return ggplot2 objects in gseaplot <2014-07-21, Mon>
CHANGES IN VERSION 2.3.3
------------------------
o geneSim can only accept one gene ID vector and perform as mgeneSim in GOSemSim <2014-06-23, Mon>
o update man files <2014-06-23, Mon>
CHANGES IN VERSION 2.3.2
------------------------
o bug fixed in scaleNodeColor <2014-06-08, Sun>
CHANGES IN VERSION 2.3.1
------------------------
o upgrade man file according to roxygen2 (ver 4.0.0) . <2014-05-16, Fri>
CHANGES IN VERSION 1.99.6
------------------------
o bug fixed in EXTID2NAME. <2013-09-28, Sat>
CHANGES IN VERSION 1.99.5
------------------------
o fixed in calculating M when only one categroy presented, the object was matrix insted of list. <2013-09-16, Mon>
CHANGES IN VERSION 1.99.4
------------------------
o export gsea function <2013-07-10, Wed>
CHANGES IN VERSION 1.99.3
------------------------
o extend EXTID2NAME to support 20 species <2013-07-09, Tue>
o update vignette. <2013-07-09, Tue>
CHANGES IN VERSION 1.99.1
------------------------
o convert vignette file to knitr Sweave. <2013-06-24, Mon>
CHANGES IN VERSION 1.99.0
------------------------
o extent ggplot to support enrichResult by implementing fortify method. <2013-05-22, Wed>
o re-implement barplot.enrichResult. <2013-05-23, Thu>
o enrich.internal support user specifiy background by parameter universe. <2013-05-24, Fri>
o implement Gene Set Enrichment Analysis algorithm. <2013-05-29, Wed>
o change setReadable to support groupGO of clusterProfiler. <2013-05-29, Wed>
o fixed mclapply not support Windows platform issue. <2013-05-30, Fri>
o rename logFC parameter to foldChange. <2013-06-13, Thu>
CHANGES IN VERSION 1.7.1
------------------------
o use geom_bar(stat="identity") instead of geom_bar() in barplot for explicitly mapping y value. <2013-05-08, Wed>
o bug fixed when qvalue can't calculated. <2013-05-02, Thu>
o bug fixed of enrich.internal, drop those genes that without annotation when calculating sample gene number. <2013-05-02, Thu>
o change some code to satisfy ReactomePA <2013-03-27, Wed>
CHANGES IN VERSION 1.5.1
------------------------
o bug fixed in enrich.internal, now return NA rather than throw error, if gene have no ontology annotation <2013-01-22, Fri>
CHANGES IN VERSION 1.3.2
------------------------
o update codes of plot functions accompaning with ggplot2 (version 0.9.2) <2012-09-06, Thu>
o update cnetplot corresponding to igraph version 0.6 <2012-07-11, Wed>
o parameter showCategory now support term ID vector <2012-07-11, Wed>
o import termSim and combineScores from GOSemSim. <2012-06,14, Thu>
o optimize setReadable <2012-05-09, Wed>
o bug fixed of setReadable method. For those unmapped genes, return the original gene ID. <2012-05-15, Tue>
o fill color in barplot for Ontology classification. <2012-05-22, Tue>
o update color scale of cnetplot <2012-06-18, Mon>
CHANGES IN VERSION 1.3.1
------------------------
o update color scheme of cnetplot <2012-04-10, Tue>
o add simplot for plotting semantic similarity matrix <2012-04-20, Fri>
o bug fixed of combineScore function for DO semantic similarity matrix
which containing NA rows of NA coloumns <2012-04-20, Fri>
o export doSim and geneSim functions <2012-04-20, Fri>
CHANGES IN VERSION 1.1.12
------------------------
o implement barplot for enrichResult <2012-03-18, Sun>
o bug fixed for setReadable method <2012-03-19, Mon>
o add logFC parameter for cnet plot, support color gene nodes by
their expression value (log fold change) <2012-03-21, Wed>
o add mapping entrezgene ID and gene Name for organisms
other than human, mouse and yeast. <2012-03-22, Thu>
o bug fixed for attempt to name logFC, when it is NULL. <2012-03-22, Thu>
o optimized readable method. <2012-03-26, Mon>
CHANGES IN VERSION 1.1.11
------------------------
o setReadable method for mapping gene ID to gene Symbol in enrichResult instance. <2012-03-12, Mon>
o export method show. <2012-03-12, Mon>
CHANGES IN VERSION 1.1.10
------------------------
o import plot summary from stats4, for BiocGenerics (version 0.1.10) removed them <2012-03-03, Sat>
o Add DO2ALLEG and EG2ALLDO, for mapping undirecte annotation. <2012-03-03, Sat>
o update vignette <2012-03-06, Tue>
CHANGES IN VERSION 1.1.9
------------------------
o fixed BibTeX database file .bib.
month = , must be month = someMonth, or totally deleted,
leave it blank will cause texi2dvi failed. <2012-03-01, Thu>
o update IC data and DO-EG mapping data. <2012-03-01, Thu>
CHANGES IN VERSION 1.1.8
------------------------
o update vignette, add semantic similarity algorithms' details. <2012-02-28, Tue>
CHANGES IN VERSION 1.1.7
------------------------
o fixed warnings concerning documents of plot generics. <2012-02-27, Mon>
o import summary generic from BiocGenerics instead of stats4. <2012-02-27, Mon>
CHANGES IN VERSION 1.1.6
------------------------
o defined S3 generic for ALLEXTID, EXTID2NAME, EXTID2TERMID, TERM2NAME,
and TERMID2EXTID. <2012-02-26, Sun>
o update roxygen and regenerate man file. <2012-02-26, Sun>
o import S4 generics of plot from BiocGenerics. <2012-02-26, Sun>
CHANGES IN VERSION 1.1.5
------------------------
o add S4 method of plot, which accept parameter type = "cnet",
and call cnetplot.enrichResult method. <2012-02-23, Thu>
o add S3 method cnetplot.enrichResult for plotting enrichResult object.
<2012-02-23, Thu>
o define cnetplot function for category-gene network visualization. <2012-02-23, Thu>
o remove generic definition of show and summary,
import show from methods and summary from stats4 <2012-02-23, Thu>
o redefine functions as S3 methods for mapping ID among gene and Term.
this will make enrich.internal which calling these mapping function more robust
<2012-02-23, Thu>
CHANGES IN VERSION 1.1.4
------------------------
o add Enrichment Analysis session in vignette. <2012-02-22, Wed>
o optimize enrichDO, ten time faster. <2012-02-22, Wed>
o separate code of enrichDO to enrich.internal, make it more general,
and can be applied to other ontology. <2012-02-22, Wed>
o rename enrichDOResult class to enrichResult and add slot geneInCategory. <2012-02-22, Wed>
o export infoContentMethod and wangMethod. <2012-02-22, Wed>
CHANGES IN VERSION 1.1.3
------------------------
o update infoContentMethod to make it consistent between DOSE and GOSemSim. <2011-12-31, Sat>
CHANGES IN VERSION 1.1.2
------------------------
o change to using roxygen for generating Rd docs
CHANGES IN VERSION 1.1.1
------------------------
o add function rebuildAnnoData
o update Disease-Gene Mapping data
CHANGES IN VERSION 0.99.7
------------------------
o fixed bug in .SemVal_internal
CHANGES IN VERSION 0.99.6
------------------------
o Use qvalue instead of fdrtool to calculate qvalues.