-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathNEWS
612 lines (376 loc) · 14.9 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
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
CHANGES IN VERSION 1.5.3
------------------------
o Changed `buildDataFromGraph()` so that it looks for organismal
annotations in `keggInfo()`.
o If `ncbi-geneid` was not available,
`buildDataFromGraph()` would crash with 404. Now, it can use
`ncbi-proteinid` if `ncbi-geneid` is missing.
o Discovered by LY by building db for `"cvi"`
o Small update on `sanitise()`
CHANGES IN VERSION 1.4.2/1.5.2
------------------------
o **The REST KEGG service changed and modules are no longer listable
by organism**. `FELLA` now chooses modules that have at least one
organismal gene. This seems equivalent to picking the modules
from `keggLink("genome", "module")`, but the latter is slow (90s).
CHANGES IN VERSION 1.4.1/1.5.1
------------------------
o Fixed bug in vignette due to changes in `biomaRt`
CHANGES IN VERSION 1.3.1
------------------------
o Fixed main vignette title to match that of paper
o Fixed `Unicode char' (U+301)` error (had a tilde as `\'\i` in bibfile)
o Added citation to BMC article
CHANGES IN VERSION 1.1.6
------------------------
o Fixed vignette indices
CHANGES IN VERSION 1.1.5
------------------------
o Added full vignette on the zebrafish dataset
o Small modifications to the Mus musculus vignette
CHANGES IN VERSION 1.1.4
------------------------
o Added a full vignette showing a case study on Mus musculus
o Functions `getCom` and `getGraph` are exported now
o Added `DT` and other packages to `suggests`
o Small fixes for `BiocCheck`
CHANGES IN VERSION 1.1.3
------------------------
o Version 1.1.2 did not skip such test
CHANGES IN VERSION 1.1.2
------------------------
o Disabled `buildGraphFromKEGGREST` test in 32-bit Windows due to
its memory usage
CHANGES IN VERSION 0.99.6
------------------------
o Small corrections in vignette
o Removed `rm` calls
CHANGES IN VERSION 0.99.5
------------------------
o Small correction in vignette
o Version bump to see if bioc build is bugged
CHANGES IN VERSION 0.99.4
------------------------
o Moved contents of `NEWS.md` to NEWS
o Deleted most of `data-raw` folder, moved the rest to `inst/script`
o Removed redundant `Authors` field in DESCRIPTION
o Removed `class(data) != "FELLA.DATA"` by using built-in
`is.FELLA.DATA`
CHANGES IN VERSION 0.99.3
------------------------
o Version bump (biomaRt down?)
CHANGES IN VERSION 0.99.2
------------------------
o Fixed more doc links
CHANGES IN VERSION 0.99.1
------------------------
o Fixed doc links (hopefully)
o Updated funding in vignette
o Travis will only test the devel branch
CHANGES IN VERSION 0.99.0
------------------------
o Submission to Bioconductor
CHANGES IN VERSION 0.5.14
------------------------
o Small bugs
CHANGES IN VERSION 0.5.13
------------------------
o Small bug fixes
CHANGES IN VERSION 0.5.12
------------------------
o Small bug fixes
CHANGES IN VERSION 0.5.11
------------------------
o Fixed calls to `sapply` and `1:n`
CHANGES IN VERSION 0.5.10
------------------------
o Adding GO CC is now in `dontrun`, takes too long (12s)
CHANGES IN VERSION 0.5.9
------------------------
o Fixed vignette: converted pdf images to eps and added them
CHANGES IN VERSION 0.5.8
------------------------
o Removed `broser()` calls
o Removed some commented code
o Expanded doc on `launchApp`
o Removed the old gone report functionality in the app
(might bring it back eventually)
o Added captures of the graphical interface to the main vignette
CHANGES IN VERSION 0.5.7
------------------------
o Slight changes in vignette (affiliations)
o Fixed `generateEnzymesTable`: now it can also add the
GO terms inside each enzyme
o Modified `addGOToGraph`: now it will add only the GO labels,
without similarity score, provided that `GOterm = NULL`
o Improved doc in result exports: `generateResultsTable`,
`generateEnzymesTable`, `generateResultsGraph`,
`addGOToGraph` and `plotGraph`.
- Merged all the doc
- Added references
- Expanded details
CHANGES IN VERSION 0.5.6
------------------------
o Improved doc in enrichment techniques:
- Merged 5 functions: `defineCompounds`, `runHypergeom`,
`runDiffusion`, `runPagerank`, `enrich`
- Expanded details: formulation, how to compute scores,
null model
- Added references
- Centralised examples
o References are now in template files
CHANGES IN VERSION 0.5.5
------------------------
o Improved doc in `FELLA.DATA` object creation
- Fused 3 functions
- Added references
- Expanded details
CHANGES IN VERSION 0.5.4
------------------------
o Added progress bars to shiny app for:
- Loading database
- Enriching
- Adding GO similarity
o Added simple legend for GO similarity
CHANGES IN VERSION 0.5.3
------------------------
o Added `CITATION` file
o Added some cites to doc
CHANGES IN VERSION 0.5.2
------------------------
o Shiny app
- Fixed bug: table not showing up
- Documentation has been improved
- Fixed bug: empty network led to error
- Now exporting a network takes into account
`thresholdConnectedComponent` as well (it did not until now)
- Modified logo size and title
CHANGES IN VERSION 0.5.1
------------------------
o Small modifications on Travis and `is-.R`
CHANGES IN VERSION 0.5.0
------------------------
o Fixed bibliography in vignette
o Fixed missing table in vignette
o Changed mechanisms when handling existing directories.
Now the writing is stopped instead of overwriting and the
automatic names are more meaningful.
o New naming convention for databases.
Meaningful names with creation date, organism and KEGG version.
o Updated unit testing and argument checking accordingly
CHANGES IN VERSION 0.4.13
------------------------
o Temporarily downgraded R dependency to version 4.3
o Bug on the `biomaRt` query was actually due to their
package being outdated. Updating fixed it.
o Small changes in functions (exports) to pass `check()`
o Small fixes on Shiny App
o Added vignette
CHANGES IN VERSION 0.4.12
------------------------
o Travis modification
CHANGES IN VERSION 0.4.11
------------------------
o Small changes on functions and DESCRIPTION
CHANGES IN VERSION 0.4.10
------------------------
o Trying Travis
CHANGES IN VERSION 0.4.9
------------------------
o Small changes in plotting functions
CHANGES IN VERSION 0.4.8
------------------------
o Fixed the `FELLA.sample` file so that it contains the metadata
o Added the `getInfo` function for getting the metabata,
with corresponding unit testing
o Fixed minor writing mistakes
o `loadMatrix` can no longer be `"all"`
o `AllArguments.R` now has `loadMatrix`, `databaseDir`, `internalDir`
o Shiny app:
- Fixed the database error when no database is present
- Fixed table error when the graph was empty (e.g. hypergeom)
- Adding a GO term is now functional again.
Added several biomaRt/GO options.
- GO term changes plot legend
- Changes in the UI (text, new widgets for GO term)
- GO example autofills all the new widgets
CHANGES IN VERSION 0.4.7
------------------------
o Improved vignette text and added Bioconductor style
o Added `BiocStyle` as a dependency
To do:
o General check of arguments and documentation
o Quantitative input?
o Elaborate on this vignette or build another one for publication
CHANGES IN VERSION 0.4.6
------------------------
o Removed the infamous `splitByCC` part (from `checkArguments`,
the conditional on the `plot` method and from the vignette)
o Now the option is to filter out small CCs but still work
with a single graph (`thresholdConnectedComponent` still exists).
Therefore, function `generateResultsGraph` can only return
a graph, being more intuitive.
CHANGES IN VERSION 0.4.5
------------------------
o Modified size p-value computation.
Now it is more efficient and consistent
CHANGES IN VERSION 0.4.4
------------------------
o Fused `checkArguments` into `AllArguments.R`
o Deleted the generic `summary` as it is not necessary.
Now the same can be achieved using `show` only, and this avoids
method dispatch issues.
CHANGES IN VERSION 0.4.3
------------------------
o Added the `summary` method for `FELLA.DATA` objects
o Fixed some dependencies in methods
o Separated `mytriangle` in function `plotGraph`
o Renamed functions (`is-.R`, `plotLegend.R`)
o Updated sample data documentation
CHANGES IN VERSION 0.4.2
------------------------
o Added doc template for the statistical normalisation
o Removed p-values from table
o Improved `generateResultsTable` function
o Improved `runDiffusion` and `runPagerank` at the code level and
avoided checking arguments
CHANGES IN VERSION 0.4.1
------------------------
o Added accessor to `status` and substituted all the calls
o Addition of GO terms works
CHANGES IN VERSION 0.4.0
------------------------
o Removed some superfluous arguments: askplots, filename, BIMODAL
o Aggregated `get-.R` and `list-.R` functions in single files
o Cleaned part of: `AllMethods`, `exportResults`, `generate-`
o Fixed unit testing
o Fixed runnable examples
o Fixed vignette
o Rebuilt example data
o Improved argument handling. `method` can no longer be `"all"` and
handles a unique method now, but `methods`
can pass a vector of methods instead
o Passes `check()` and `BiocCheck(".")`
CHANGES IN VERSION 0.3.3
------------------------
o Improved argument documentation (still work to do)
o Fused individual dummy functions that contained the commented parameters
o Added `list-()` functions
o Removed `p.adjust` from diffusion and pagerank
o Improved unit testing
To do:
o Fix documentation of changed functions
o Try to better isolate functions (e.g. `plot` and `generateResultsGraph`
do too many things at once...)
o Quantitative input?
o Delete repetitive code
o Use `checkArguments` in main functions
o Improve `AllMethods`: use accessors, clean code...
CHANGES IN VERSION 0.3.2
------------------------
o Switched from `pValues` to `pScores` (except in `hypergeom`)
CHANGES IN VERSION 0.3.1
------------------------
o Removed `rcytoscapejs` dependency
CHANGES IN VERSION 0.3.0
------------------------
o Fixed vignette
o Modifications to several functions, addressing:
- Proper handling of GO labels - now can be used in many species
- `addCellularComponentToGraph` is now `addGOToGraph`
- New dependency: biomaRt
- Plotting functions have been simplified, but still need work
- Graph building has been improved
o Shiny app:
- Removed tabs, has only 4 now
- Left only interactive plot
- Table is now from `DT`
To do:
o Fix documentation of changed functions
o Try to better isolate functions (e.g. `plot` and `generateResultsGraph`
do too many things at once...)
o Quantitative input?
o Improve function documentation (use templates) to supress warnings
o Change `rcytoscapejs` dependency to `visNetwork` (in CRAN)
o What to do about the p-values?
CHANGES IN VERSION 0.2.6
------------------------
o Fixed indentation
o Fixed long lines
o Added NEWS file
o Fixed examples
To do:
o Vignette breaks, top priority
o Quantitative input?
o Improve function documentation (use templates) to supress warnings
o Change `rcytoscapejs` dependency to `visNetwork` (in CRAN)
o What to do about the p-values?
CHANGES IN VERSION 0.2.5
------------------------
Some minor changes to accomodate Bioconductor's standards:
o Update `R` version
o Add `R` file to the `testthat` folder
o Add GO biocView
To do from Bioconductor:
o Vignette breaks
o Add NEWS file
o Fix indentation
o Fix long lines (<80)
o Add runnable examples:
- buildDataFromGraph
- buildGraphFromKEGGREST
- loadKEGGdata
To do:
o Quantitative input?
o Improve function documentation (use templates) to supress warnings
o Change `rcytoscapejs` dependency to `visNetwork` (in CRAN)
CHANGES IN VERSION 0.2.4
------------------------
o Minor tweaks in the plotting function. Has more flexibility
and can use `tkplot` as well (for image generation purposes),
or force layout. This function should be really improved,
it's not that hard...
CHANGES IN VERSION 0.2.3
------------------------
o Fixed CREB website link
o Added the option to specify the damping factor in pagerank
o Changed default damping factor to 0.85
CHANGES IN VERSION 0.2.2
------------------------
o Fixed table export (`stringsAsFactors` was not
disabled when creating the data.frame).
o Added the function `generateEnzymesTable` to build a table with the
EC numbers, along with the genes (entrez) within them and the associated
GO labels (http://www.geneontology.org/).
o The shiny app exports tables with the full enzyme data and
simply as a text gene list as well.
CHANGES IN VERSION 0.2.1
------------------------
The shiny app has been updated.
o Now the rcytoscape part has clickable links.
This is due to a change in the
r-cytoscape.js (https://github.com/cytoscape/r-cytoscape.js/)
package that changes the `href` node attribute to `tooltip`.
o The colors and shapes have been updated as well, to be consistent with
our notation.
To do:
o The labels of the nodes are not sorted by length.
Short labels can be really weird...
CHANGES IN VERSION 0.2.0
------------------------
Added the shiny app as a developer option. It requires the following packages:
o shiny
o DT
o xtable
o knitr
o rcytoscapejs
CHANGES IN VERSION 0.0.999
------------------------
+ This is the first version of this package. It contains:
o Basic enrichment functions: hypergeom, diffusion, pagerank
o Null models: normal or Monte Carlo
o Export options: to tables or graphs
o Plotting capabilities
o Possibility of custom background
+ Further versions should include interactive plots and
applications for an easier usage