-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathrenv.lock
8596 lines (8596 loc) · 458 KB
/
renv.lock
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
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
{
"R": {
"Version": "4.4.1",
"Repositories": [
{
"Name": "BioCsoft",
"URL": "https://bioconductor.org/packages/3.20/bioc"
},
{
"Name": "BioCann",
"URL": "https://bioconductor.org/packages/3.20/data/annotation"
},
{
"Name": "BioCexp",
"URL": "https://bioconductor.org/packages/3.20/data/experiment"
},
{
"Name": "BioCworkflows",
"URL": "https://bioconductor.org/packages/3.20/workflows"
},
{
"Name": "BioCbooks",
"URL": "https://bioconductor.org/packages/3.20/books"
},
{
"Name": "CRAN",
"URL": "https://packagemanager.posit.co/cran/latest"
}
]
},
"Bioconductor": {
"Version": "3.20"
},
"Packages": {
"ALL": {
"Package": "ALL",
"Version": "1.48.0",
"Source": "Bioconductor",
"Title": "A data package",
"Date": "2009-07-22",
"Author": "Xiaochun Li",
"Description": "Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions)",
"Maintainer": "Robert Gentleman <[email protected]>",
"License": "Artistic-2.0",
"Depends": [
"R (>= 2.10)",
"Biobase (>= 2.5.5)"
],
"Suggests": [
"rpart"
],
"biocViews": "ExperimentData, CancerData, LeukemiaCancerData",
"git_url": "https://git.bioconductor.org/packages/ALL",
"git_branch": "RELEASE_3_20",
"git_last_commit": "740783d",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no"
},
"AnnotationDbi": {
"Package": "AnnotationDbi",
"Version": "1.68.0",
"Source": "Bioconductor",
"Title": "Manipulation of SQLite-based annotations in Bioconductor",
"Description": "Implements a user-friendly interface for querying SQLite-based annotation data packages.",
"biocViews": "Annotation, Microarray, Sequencing, GenomeAnnotation",
"URL": "https://bioconductor.org/packages/AnnotationDbi",
"Video": "https://www.youtube.com/watch?v=8qvGNTVz3Ik",
"BugReports": "https://github.com/Bioconductor/AnnotationDbi/issues",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"Author": "Hervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li",
"Maintainer": "Bioconductor Package Maintainer <[email protected]>",
"Depends": [
"R (>= 2.7.0)",
"methods",
"stats4",
"BiocGenerics (>= 0.29.2)",
"Biobase (>= 1.17.0)",
"IRanges"
],
"Imports": [
"DBI",
"RSQLite",
"S4Vectors (>= 0.9.25)",
"stats",
"KEGGREST"
],
"Suggests": [
"utils",
"hgu95av2.db",
"GO.db",
"org.Sc.sgd.db",
"org.At.tair.db",
"RUnit",
"TxDb.Hsapiens.UCSC.hg19.knownGene",
"org.Hs.eg.db",
"reactome.db",
"AnnotationForge",
"graph",
"EnsDb.Hsapiens.v75",
"BiocStyle",
"knitr"
],
"VignetteBuilder": "knitr",
"Collate": "00RTobjs.R AllGenerics.R AllClasses.R unlist2.R utils.R SQL.R FlatBimap.R AnnDbObj-lowAPI.R Bimap.R GOTerms.R BimapFormatting.R Bimap-envirAPI.R flatten.R methods-AnnotationDb.R methods-SQLiteConnection.R methods-geneCentricDbs.R methods-geneCentricDbs-keys.R methods-ReactomeDb.R methods-OrthologyDb.R loadDb.R createAnnObjs-utils.R createAnnObjs.NCBIORG_DBs.R createAnnObjs.NCBICHIP_DBs.R createAnnObjs.ORGANISM_DB.R createAnnObjs.YEASTCHIP_DB.R createAnnObjs.COELICOLOR_DB.R createAnnObjs.ARABIDOPSISCHIP_DB.R createAnnObjs.MALARIA_DB.R createAnnObjs.YEAST_DB.R createAnnObjs.YEASTNCBI_DB.R createAnnObjs.ARABIDOPSIS_DB.R createAnnObjs.GO_DB.R createAnnObjs.KEGG_DB.R createAnnObjs.PFAM_DB.R AnnDbPkg-templates-common.R AnnDbPkg-checker.R print.probetable.R makeMap.R inpIDMapper.R test_AnnotationDbi_package.R",
"git_url": "https://git.bioconductor.org/packages/AnnotationDbi",
"git_branch": "RELEASE_3_20",
"git_last_commit": "6a2aa33",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no"
},
"AnnotationFilter": {
"Package": "AnnotationFilter",
"Version": "1.30.0",
"Source": "Bioconductor",
"Title": "Facilities for Filtering Bioconductor Annotation Resources",
"Authors@R": "c( person(\"Martin\", \"Morgan\", email = \"[email protected]\", role = \"aut\"), person(\"Johannes\", \"Rainer\", email = \"[email protected]\", role = \"aut\"), person(\"Joachim\", \"Bargsten\", email = \"[email protected]\", role = \"ctb\"), person(\"Daniel\", \"Van Twisk\", email = \"[email protected]\", role = \"ctb\"), person(\"Bioconductor Package\", \"Maintainer\", email=\"[email protected]\", role = \"cre\"))",
"URL": "https://github.com/Bioconductor/AnnotationFilter",
"BugReports": "https://github.com/Bioconductor/AnnotationFilter/issues",
"Description": "This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.",
"Depends": [
"R (>= 3.4.0)"
],
"Imports": [
"utils",
"methods",
"GenomicRanges",
"lazyeval"
],
"Suggests": [
"BiocStyle",
"knitr",
"testthat",
"RSQLite",
"org.Hs.eg.db",
"rmarkdown"
],
"VignetteBuilder": "knitr",
"License": "Artistic-2.0",
"biocViews": "Annotation, Infrastructure, Software",
"Encoding": "UTF-8",
"RoxygenNote": "6.0.1",
"Collate": "'AllGenerics.R' 'AnnotationFilter.R' 'AnnotationFilterList.R' 'translate-utils.R'",
"git_url": "https://git.bioconductor.org/packages/AnnotationFilter",
"git_branch": "RELEASE_3_20",
"git_last_commit": "1204cb5",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no",
"Author": "Martin Morgan [aut], Johannes Rainer [aut], Joachim Bargsten [ctb], Daniel Van Twisk [ctb], Bioconductor Package Maintainer [cre]",
"Maintainer": "Bioconductor Package Maintainer <[email protected]>"
},
"BH": {
"Package": "BH",
"Version": "1.87.0-1",
"Source": "Repository",
"Type": "Package",
"Title": "Boost C++ Header Files",
"Date": "2024-12-17",
"Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"John W.\", \"Emerson\", role = \"aut\"), person(\"Michael J.\", \"Kane\", role = \"aut\", comment = c(ORCID = \"0000-0003-1899-6662\")))",
"Description": "Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN packages. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided. As of release 1.84.0-0, the following Boost libraries are included: 'accumulators' 'algorithm' 'align' 'any' 'atomic' 'beast' 'bimap' 'bind' 'circular_buffer' 'compute' 'concept' 'config' 'container' 'date_time' 'detail' 'dynamic_bitset' 'exception' 'flyweight' 'foreach' 'functional' 'fusion' 'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io' 'iostreams' 'iterator' 'lambda2' 'math' 'move' 'mp11' 'mpl' 'multiprecision' 'numeric' 'pending' 'phoenix' 'polygon' 'preprocessor' 'process' 'propery_tree' 'qvm' 'random' 'range' 'scope_exit' 'smart_ptr' 'sort' 'spirit' 'tuple' 'type_traits' 'typeof' 'unordered' 'url' 'utility' 'uuid'.",
"License": "BSL-1.0",
"URL": "https://github.com/eddelbuettel/bh, https://dirk.eddelbuettel.com/code/bh.html",
"BugReports": "https://github.com/eddelbuettel/bh/issues",
"NeedsCompilation": "no",
"Author": "Dirk Eddelbuettel [aut, cre] (<https://orcid.org/0000-0001-6419-907X>), John W. Emerson [aut], Michael J. Kane [aut] (<https://orcid.org/0000-0003-1899-6662>)",
"Maintainer": "Dirk Eddelbuettel <[email protected]>",
"Repository": "CRAN",
"Encoding": "UTF-8"
},
"Biobase": {
"Package": "Biobase",
"Version": "2.66.0",
"Source": "Bioconductor",
"Title": "Biobase: Base functions for Bioconductor",
"Description": "Functions that are needed by many other packages or which replace R functions.",
"biocViews": "Infrastructure",
"URL": "https://bioconductor.org/packages/Biobase",
"BugReports": "https://github.com/Bioconductor/Biobase/issues",
"License": "Artistic-2.0",
"Authors@R": "c( person(\"R.\", \"Gentleman\", role=\"aut\"), person(\"V.\", \"Carey\", role = \"aut\"), person(\"M.\", \"Morgan\", role=\"aut\"), person(\"S.\", \"Falcon\", role=\"aut\"), person(\"Haleema\", \"Khan\", role = \"ctb\", comment = \"'esApply' and 'BiobaseDevelopment' vignette translation from Sweave to Rmarkdown / HTML\" ), person(\"Bioconductor Package Maintainer\", role = \"cre\", email = \"[email protected]\" ))",
"Suggests": [
"tools",
"tkWidgets",
"ALL",
"RUnit",
"golubEsets",
"BiocStyle",
"knitr",
"limma"
],
"Depends": [
"R (>= 2.10)",
"BiocGenerics (>= 0.27.1)",
"utils"
],
"Imports": [
"methods"
],
"VignetteBuilder": "knitr",
"LazyLoad": "yes",
"Collate": "tools.R strings.R environment.R vignettes.R packages.R AllGenerics.R VersionsClass.R VersionedClasses.R methods-VersionsNull.R methods-VersionedClass.R DataClasses.R methods-aggregator.R methods-container.R methods-MIAxE.R methods-MIAME.R methods-AssayData.R methods-AnnotatedDataFrame.R methods-eSet.R methods-ExpressionSet.R methods-MultiSet.R methods-SnpSet.R methods-NChannelSet.R anyMissing.R rowOp-methods.R updateObjectTo.R methods-ScalarObject.R zzz.R",
"git_url": "https://git.bioconductor.org/packages/Biobase",
"git_branch": "RELEASE_3_20",
"git_last_commit": "2cd604f",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "yes",
"Author": "R. Gentleman [aut], V. Carey [aut], M. Morgan [aut], S. Falcon [aut], Haleema Khan [ctb] ('esApply' and 'BiobaseDevelopment' vignette translation from Sweave to Rmarkdown / HTML), Bioconductor Package Maintainer [cre]",
"Maintainer": "Bioconductor Package Maintainer <[email protected]>"
},
"BiocBaseUtils": {
"Package": "BiocBaseUtils",
"Version": "1.8.0",
"Source": "Bioconductor",
"Title": "General utility functions for developing Bioconductor packages",
"Authors@R": "c( person(\"Marcel\", \"Ramos\", , \"[email protected]\", c(\"aut\", \"cre\"), c(ORCID = \"0000-0002-3242-0582\") ), person(\"Martin\", \"Morgan\", , \"[email protected]\", \"ctb\" ), person(\"Hervé\", \"Pagès\", , \"[email protected]\", \"ctb\") )",
"Description": "The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.",
"Imports": [
"methods",
"utils"
],
"Depends": [
"R (>= 4.2.0)"
],
"Suggests": [
"knitr",
"rmarkdown",
"BiocStyle",
"tinytest"
],
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"biocViews": "Software, Infrastructure",
"BugReports": "https://www.github.com/Bioconductor/BiocBaseUtils/issues",
"Roxygen": "list(markdown = TRUE)",
"RoxygenNote": "7.3.2",
"VignetteBuilder": "knitr",
"Date": "2024-08-22",
"git_url": "https://git.bioconductor.org/packages/BiocBaseUtils",
"git_branch": "RELEASE_3_20",
"git_last_commit": "ad54d83",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no",
"Author": "Marcel Ramos [aut, cre] (<https://orcid.org/0000-0002-3242-0582>), Martin Morgan [ctb], Hervé Pagès [ctb]",
"Maintainer": "Marcel Ramos <[email protected]>"
},
"BiocGenerics": {
"Package": "BiocGenerics",
"Version": "0.52.0",
"Source": "Bioconductor",
"Title": "S4 generic functions used in Bioconductor",
"Description": "The package defines many S4 generic functions used in Bioconductor.",
"biocViews": "Infrastructure",
"URL": "https://bioconductor.org/packages/BiocGenerics",
"BugReports": "https://github.com/Bioconductor/BiocGenerics/issues",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"Author": "The Bioconductor Dev Team",
"Maintainer": "Hervé Pagès <[email protected]>",
"Depends": [
"R (>= 4.0.0)",
"methods",
"utils",
"graphics",
"stats"
],
"Imports": [
"methods",
"utils",
"graphics",
"stats"
],
"Suggests": [
"Biobase",
"S4Vectors",
"IRanges",
"S4Arrays",
"SparseArray",
"DelayedArray",
"HDF5Array",
"GenomicRanges",
"pwalign",
"Rsamtools",
"AnnotationDbi",
"affy",
"affyPLM",
"DESeq2",
"flowClust",
"MSnbase",
"annotate",
"RUnit"
],
"Collate": "S3-classes-as-S4-classes.R utils.R normarg-utils.R replaceSlots.R aperm.R append.R as.data.frame.R as.list.R as.vector.R cbind.R do.call.R duplicated.R eval.R Extremes.R format.R funprog.R get.R grep.R is.unsorted.R lapply.R mapply.R match.R mean.R nrow.R order.R paste.R rank.R rep.R row_colnames.R saveRDS.R sets.R sort.R start.R subset.R t.R table.R tapply.R unique.R unlist.R unsplit.R relist.R var.R which.R which.min.R boxplot.R image.R density.R IQR.R mad.R residuals.R weights.R xtabs.R annotation.R combine.R containsOutOfMemoryData.R dbconn.R dge.R dims.R fileName.R normalize.R Ontology.R organism_species.R path.R plotMA.R plotPCA.R score.R strand.R toTable.R type.R updateObject.R testPackage.R zzz.R",
"git_url": "https://git.bioconductor.org/packages/BiocGenerics",
"git_branch": "RELEASE_3_20",
"git_last_commit": "1422115",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no"
},
"BiocIO": {
"Package": "BiocIO",
"Version": "1.16.0",
"Source": "Bioconductor",
"Title": "Standard Input and Output for Bioconductor Packages",
"Authors@R": "c( person(\"Martin\", \"Morgan\", role = \"aut\"), person(\"Michael\", \"Lawrence\", role = \"aut\"), person(\"Daniel\", \"Van Twisk\", role = \"aut\"), person(\"Marcel\", \"Ramos\", , \"[email protected]\", \"cre\", c(ORCID = \"0000-0002-3242-0582\") ))",
"Description": "The `BiocIO` package contains high-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"Roxygen": "list(markdown = TRUE)",
"RoxygenNote": "7.3.2",
"Depends": [
"R (>= 4.3.0)"
],
"Imports": [
"BiocGenerics",
"S4Vectors",
"methods",
"tools"
],
"Suggests": [
"testthat",
"knitr",
"rmarkdown",
"BiocStyle"
],
"Collate": "'BiocFile.R' 'import_export.R' 'compression.R' 'utils.R'",
"VignetteBuilder": "knitr",
"biocViews": "Annotation,DataImport",
"BugReports": "https://github.com/Bioconductor/BiocIO/issues",
"Date": "2024-08-22",
"git_url": "https://git.bioconductor.org/packages/BiocIO",
"git_branch": "RELEASE_3_20",
"git_last_commit": "8e80624",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no",
"Author": "Martin Morgan [aut], Michael Lawrence [aut], Daniel Van Twisk [aut], Marcel Ramos [cre] (<https://orcid.org/0000-0002-3242-0582>)",
"Maintainer": "Marcel Ramos <[email protected]>"
},
"BiocManager": {
"Package": "BiocManager",
"Version": "1.30.25",
"Source": "Repository",
"Title": "Access the Bioconductor Project Package Repository",
"Description": "A convenient tool to install and update Bioconductor packages.",
"Authors@R": "c( person(\"Martin\", \"Morgan\", email = \"[email protected]\", role = \"aut\", comment = c(ORCID = \"0000-0002-5874-8148\")), person(\"Marcel\", \"Ramos\", email = \"[email protected]\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3242-0582\")))",
"Imports": [
"utils"
],
"Suggests": [
"BiocVersion",
"BiocStyle",
"remotes",
"rmarkdown",
"testthat",
"withr",
"curl",
"knitr"
],
"URL": "https://bioconductor.github.io/BiocManager/",
"BugReports": "https://github.com/Bioconductor/BiocManager/issues",
"VignetteBuilder": "knitr",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"RoxygenNote": "7.3.1",
"NeedsCompilation": "no",
"Author": "Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>), Marcel Ramos [aut, cre] (<https://orcid.org/0000-0002-3242-0582>)",
"Maintainer": "Marcel Ramos <[email protected]>",
"Repository": "CRAN"
},
"BiocParallel": {
"Package": "BiocParallel",
"Version": "1.40.0",
"Source": "Bioconductor",
"Type": "Package",
"Title": "Bioconductor facilities for parallel evaluation",
"Authors@R": "c( person(\"Martin\", \"Morgan\", email = \"[email protected]\", role=c(\"aut\", \"cre\")), person(\"Jiefei\", \"Wang\", role = \"aut\"), person(\"Valerie\", \"Obenchain\", role=\"aut\"), person(\"Michel\", \"Lang\", email=\"[email protected]\", role=\"aut\"), person(\"Ryan\", \"Thompson\", email=\"[email protected]\", role=\"aut\"), person(\"Nitesh\", \"Turaga\", role=\"aut\"), person(\"Aaron\", \"Lun\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", role = \"ctb\"), person(\"Madelyn\", \"Carlson\", role = \"ctb\", comment = \"Translated 'Random Numbers' vignette from Sweave to RMarkdown / HTML.\" ), person(\"Phylis\", \"Atieno\", role = \"ctb\", comment = \"Translated 'Introduction to BiocParallel' vignette from Sweave to Rmarkdown / HTML.\" ), person( \"Sergio\", \"Oller\", role = \"ctb\", comment = c( \"Improved bpmapply() efficiency.\", \"ORCID\" = \"0000-0002-8994-1549\" ) ))",
"Description": "This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.",
"URL": "https://github.com/Bioconductor/BiocParallel",
"BugReports": "https://github.com/Bioconductor/BiocParallel/issues",
"biocViews": "Infrastructure",
"License": "GPL-2 | GPL-3",
"SystemRequirements": "C++11",
"Depends": [
"methods",
"R (>= 3.5.0)"
],
"Imports": [
"stats",
"utils",
"futile.logger",
"parallel",
"snow",
"codetools"
],
"Suggests": [
"BiocGenerics",
"tools",
"foreach",
"BBmisc",
"doParallel",
"GenomicRanges",
"RNAseqData.HNRNPC.bam.chr14",
"TxDb.Hsapiens.UCSC.hg19.knownGene",
"VariantAnnotation",
"Rsamtools",
"GenomicAlignments",
"ShortRead",
"RUnit",
"BiocStyle",
"knitr",
"batchtools",
"data.table"
],
"Enhances": [
"Rmpi"
],
"Collate": "AllGenerics.R DeveloperInterface.R prototype.R bploop.R ErrorHandling.R log.R bpbackend-methods.R bpisup-methods.R bplapply-methods.R bpiterate-methods.R bpstart-methods.R bpstop-methods.R BiocParallelParam-class.R bpmapply-methods.R bpschedule-methods.R bpvec-methods.R bpvectorize-methods.R bpworkers-methods.R bpaggregate-methods.R bpvalidate.R SnowParam-class.R MulticoreParam-class.R TransientMulticoreParam-class.R register.R SerialParam-class.R DoparParam-class.R SnowParam-utils.R BatchtoolsParam-class.R progress.R ipcmutex.R worker-number.R utilities.R rng.R bpinit.R reducer.R worker.R bpoptions.R cpp11.R BiocParallel-defunct.R",
"LinkingTo": [
"BH",
"cpp11"
],
"VignetteBuilder": "knitr",
"RoxygenNote": "7.1.2",
"git_url": "https://git.bioconductor.org/packages/BiocParallel",
"git_branch": "RELEASE_3_20",
"git_last_commit": "a57b788",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "yes",
"Author": "Martin Morgan [aut, cre], Jiefei Wang [aut], Valerie Obenchain [aut], Michel Lang [aut], Ryan Thompson [aut], Nitesh Turaga [aut], Aaron Lun [ctb], Henrik Bengtsson [ctb], Madelyn Carlson [ctb] (Translated 'Random Numbers' vignette from Sweave to RMarkdown / HTML.), Phylis Atieno [ctb] (Translated 'Introduction to BiocParallel' vignette from Sweave to Rmarkdown / HTML.), Sergio Oller [ctb] (Improved bpmapply() efficiency., <https://orcid.org/0000-0002-8994-1549>)",
"Maintainer": "Martin Morgan <[email protected]>"
},
"BiocVersion": {
"Package": "BiocVersion",
"Version": "3.20.0",
"Source": "Bioconductor",
"Title": "Set the appropriate version of Bioconductor packages",
"Description": "This package provides repository information for the appropriate version of Bioconductor.",
"Authors@R": "c( person(\"Martin\", \"Morgan\", email = \"[email protected]\", role = \"aut\"), person(\"Marcel\", \"Ramos\", email = \"[email protected]\", role = \"ctb\"), person(\"Bioconductor\", \"Package Maintainer\", email = \"[email protected]\", role = c(\"ctb\", \"cre\")))",
"biocViews": "Infrastructure",
"Depends": [
"R (>= 4.4.0)"
],
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"RoxygenNote": "6.0.1",
"git_url": "https://git.bioconductor.org/packages/BiocVersion",
"git_branch": "devel",
"git_last_commit": "43c716a",
"git_last_commit_date": "2024-04-30",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no",
"Author": "Martin Morgan [aut], Marcel Ramos [ctb], Bioconductor Package Maintainer [ctb, cre]",
"Maintainer": "Bioconductor Package Maintainer <[email protected]>"
},
"Biostrings": {
"Package": "Biostrings",
"Version": "2.74.1",
"Source": "Bioconductor",
"Title": "Efficient manipulation of biological strings",
"Description": "Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.",
"biocViews": "SequenceMatching, Alignment, Sequencing, Genetics, DataImport, DataRepresentation, Infrastructure",
"URL": "https://bioconductor.org/packages/Biostrings",
"BugReports": "https://github.com/Bioconductor/Biostrings/issues",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"Authors@R": "c( person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"), email=\"[email protected]\"), person(\"Patrick\", \"Aboyoun\", role=\"aut\"), person(\"Robert\", \"Gentleman\", role=\"aut\"), person(\"Saikat\", \"DebRoy\", role=\"aut\"), person(\"Vince\", \"Carey\", role=\"ctb\"), person(\"Nicolas\", \"Delhomme\", role=\"ctb\"), person(\"Felix\", \"Ernst\", role=\"ctb\"), person(\"Wolfgang\", \"Huber\", role=\"ctb\", comment=\"'matchprobes' vignette\"), person(\"Beryl\", \"Kanali\", role=\"ctb\", comment=\"Converted 'MultipleAlignments' vignette from Sweave to RMarkdown\"), person(\"Haleema\", \"Khan\", role=\"ctb\", comment=\"Converted 'matchprobes' vignette from Sweave to RMarkdown\"), person(\"Aidan\", \"Lakshman\", role=\"ctb\"), person(\"Kieran\", \"O'Neill\", role=\"ctb\"), person(\"Valerie\", \"Obenchain\", role=\"ctb\"), person(\"Marcel\", \"Ramos\", role=\"ctb\"), person(\"Albert\", \"Vill\", role=\"ctb\"), person(\"Jen\", \"Wokaty\", role=\"ctb\", comment=\"Converted 'matchprobes' vignette from Sweave to RMarkdown\"), person(\"Erik\", \"Wright\", role=\"ctb\"))",
"Depends": [
"R (>= 4.0.0)",
"BiocGenerics (>= 0.37.0)",
"S4Vectors (>= 0.27.12)",
"IRanges (>= 2.31.2)",
"XVector (>= 0.37.1)",
"GenomeInfoDb"
],
"Imports": [
"methods",
"utils",
"grDevices",
"stats",
"crayon"
],
"LinkingTo": [
"S4Vectors",
"IRanges",
"XVector"
],
"Suggests": [
"graphics",
"pwalign",
"BSgenome (>= 1.13.14)",
"BSgenome.Celegans.UCSC.ce2 (>= 1.3.11)",
"BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11)",
"BSgenome.Hsapiens.UCSC.hg18",
"drosophila2probe",
"hgu95av2probe",
"hgu133aprobe",
"GenomicFeatures (>= 1.3.14)",
"hgu95av2cdf",
"affy (>= 1.41.3)",
"affydata (>= 1.11.5)",
"RUnit",
"BiocStyle",
"knitr",
"testthat (>= 3.0.0)",
"covr"
],
"VignetteBuilder": "knitr",
"Collate": "utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R GENETIC_CODE.R XStringCodec-class.R seqtype.R coloring.R XString-class.R XStringSet-class.R XStringSet-comparison.R XStringViews-class.R MaskedXString-class.R XStringSetList-class.R seqinfo-methods.R xscat.R XStringSet-io.R letter.R getSeq.R letterFrequency.R dinucleotideFrequencyTest.R chartr.R reverseComplement.R translate.R toComplex.R replaceAt.R replaceLetterAt.R injectHardMask.R padAndClip.R strsplit-methods.R misc.R SparseList-class.R MIndex-class.R lowlevel-matching.R match-utils.R matchPattern.R maskMotif.R matchLRPatterns.R trimLRPatterns.R matchProbePair.R matchPWM.R findPalindromes.R PDict-class.R matchPDict.R XStringPartialMatches-class.R XStringQuality-class.R QualityScaledXStringSet.R pmatchPattern.R needwunsQS.R MultipleAlignment.R matchprobes.R moved_to_pwalign.R zzz.R",
"git_url": "https://git.bioconductor.org/packages/Biostrings",
"git_branch": "RELEASE_3_20",
"git_last_commit": "b5de574",
"git_last_commit_date": "2024-12-14",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "yes",
"Author": "Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Robert Gentleman [aut], Saikat DebRoy [aut], Vince Carey [ctb], Nicolas Delhomme [ctb], Felix Ernst [ctb], Wolfgang Huber [ctb] ('matchprobes' vignette), Beryl Kanali [ctb] (Converted 'MultipleAlignments' vignette from Sweave to RMarkdown), Haleema Khan [ctb] (Converted 'matchprobes' vignette from Sweave to RMarkdown), Aidan Lakshman [ctb], Kieran O'Neill [ctb], Valerie Obenchain [ctb], Marcel Ramos [ctb], Albert Vill [ctb], Jen Wokaty [ctb] (Converted 'matchprobes' vignette from Sweave to RMarkdown), Erik Wright [ctb]",
"Maintainer": "Hervé Pagès <[email protected]>"
},
"ComplexHeatmap": {
"Package": "ComplexHeatmap",
"Version": "2.22.0",
"Source": "Bioconductor",
"Type": "Package",
"Title": "Make Complex Heatmaps",
"Date": "2024-09-24",
"Authors@R": "person(\"Zuguang\", \"Gu\", email = \"[email protected]\", role = c(\"aut\", \"cre\"), comment = c('ORCID'=\"0000-0002-7395-8709\"))",
"Depends": [
"R (>= 3.5.0)",
"methods",
"grid",
"graphics",
"stats",
"grDevices"
],
"Imports": [
"circlize (>= 0.4.14)",
"GetoptLong",
"colorspace",
"clue",
"RColorBrewer",
"GlobalOptions (>= 0.1.0)",
"png",
"digest",
"IRanges",
"matrixStats",
"foreach",
"doParallel",
"codetools"
],
"Suggests": [
"testthat (>= 1.0.0)",
"knitr",
"markdown",
"dendsort",
"jpeg",
"tiff",
"fastcluster",
"EnrichedHeatmap",
"dendextend (>= 1.0.1)",
"grImport",
"grImport2",
"glue",
"GenomicRanges",
"gridtext",
"pheatmap (>= 1.0.12)",
"gridGraphics",
"gplots",
"rmarkdown",
"Cairo",
"magick"
],
"VignetteBuilder": "knitr",
"Description": "Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.",
"biocViews": "Software, Visualization, Sequencing",
"URL": "https://github.com/jokergoo/ComplexHeatmap, https://jokergoo.github.io/ComplexHeatmap-reference/book/",
"License": "MIT + file LICENSE",
"git_url": "https://git.bioconductor.org/packages/ComplexHeatmap",
"git_branch": "RELEASE_3_20",
"git_last_commit": "bf351d6",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no",
"Author": "Zuguang Gu [aut, cre] (<https://orcid.org/0000-0002-7395-8709>)",
"Maintainer": "Zuguang Gu <[email protected]>"
},
"ConsensusClusterPlus": {
"Package": "ConsensusClusterPlus",
"Version": "1.70.0",
"Source": "Bioconductor",
"Type": "Package",
"Imports": [
"Biobase",
"ALL",
"graphics",
"stats",
"utils",
"cluster"
],
"Title": "ConsensusClusterPlus",
"Date": "2020-4-24",
"Author": "Matt Wilkerson <[email protected]>, Peter Waltman <[email protected]>",
"Maintainer": "Matt Wilkerson <[email protected]>",
"Description": "algorithm for determining cluster count and membership by stability evidence in unsupervised analysis",
"License": "GPL version 2",
"biocViews": "Software, Clustering",
"git_url": "https://git.bioconductor.org/packages/ConsensusClusterPlus",
"git_branch": "RELEASE_3_20",
"git_last_commit": "7e4ddf6",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no"
},
"DBI": {
"Package": "DBI",
"Version": "1.2.3",
"Source": "Repository",
"Title": "R Database Interface",
"Date": "2024-06-02",
"Authors@R": "c( person(\"R Special Interest Group on Databases (R-SIG-DB)\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"[email protected]\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\") )",
"Description": "A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.",
"License": "LGPL (>= 2.1)",
"URL": "https://dbi.r-dbi.org, https://github.com/r-dbi/DBI",
"BugReports": "https://github.com/r-dbi/DBI/issues",
"Depends": [
"methods",
"R (>= 3.0.0)"
],
"Suggests": [
"arrow",
"blob",
"covr",
"DBItest",
"dbplyr",
"downlit",
"dplyr",
"glue",
"hms",
"knitr",
"magrittr",
"nanoarrow (>= 0.3.0.1)",
"RMariaDB",
"rmarkdown",
"rprojroot",
"RSQLite (>= 1.1-2)",
"testthat (>= 3.0.0)",
"vctrs",
"xml2"
],
"VignetteBuilder": "knitr",
"Config/autostyle/scope": "line_breaks",
"Config/autostyle/strict": "false",
"Config/Needs/check": "r-dbi/DBItest",
"Encoding": "UTF-8",
"RoxygenNote": "7.3.1",
"Config/Needs/website": "r-dbi/DBItest, r-dbi/dbitemplate, adbi, AzureKusto, bigrquery, DatabaseConnector, dittodb, duckdb, implyr, lazysf, odbc, pool, RAthena, IMSMWU/RClickhouse, RH2, RJDBC, RMariaDB, RMySQL, RPostgres, RPostgreSQL, RPresto, RSQLite, sergeant, sparklyr, withr",
"Config/testthat/edition": "3",
"NeedsCompilation": "no",
"Author": "R Special Interest Group on Databases (R-SIG-DB) [aut], Hadley Wickham [aut], Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), R Consortium [fnd]",
"Maintainer": "Kirill Müller <[email protected]>",
"Repository": "CRAN"
},
"DOSE": {
"Package": "DOSE",
"Version": "4.0.0",
"Source": "Bioconductor",
"Type": "Package",
"Title": "Disease Ontology Semantic and Enrichment analysis",
"Authors@R": "c( person(given = \"Guangchuang\", family = \"Yu\", email = \"[email protected]\", role = c(\"aut\", \"cre\")), person(given = \"Li-Gen\", family = \"Wang\", email = \"[email protected]\", role = \"ctb\"), person(given = \"Vladislav\", family = \"Petyuk\", email = \"[email protected]\", role = \"ctb\"), person(given = \"Giovanni\", family = \"Dall'Olio\", email = \"[email protected]\", role = \"ctb\"))",
"Maintainer": "Guangchuang Yu <[email protected]>",
"Description": "This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.",
"Depends": [
"R (>= 3.5.0)"
],
"Imports": [
"AnnotationDbi",
"BiocParallel",
"fgsea",
"ggplot2",
"GOSemSim (>= 2.31.2)",
"methods",
"qvalue",
"reshape2",
"stats",
"utils",
"yulab.utils (>= 0.1.6)"
],
"Suggests": [
"prettydoc",
"clusterProfiler",
"gson (>= 0.0.5)",
"knitr",
"memoise",
"org.Hs.eg.db",
"rmarkdown",
"testthat"
],
"VignetteBuilder": "knitr",
"ByteCompile": "true",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"URL": "https://yulab-smu.top/contribution-knowledge-mining/",
"BugReports": "https://github.com/GuangchuangYu/DOSE/issues",
"biocViews": "Annotation, Visualization, MultipleComparison, GeneSetEnrichment, Pathways, Software",
"RoxygenNote": "7.3.2",
"git_url": "https://git.bioconductor.org/packages/DOSE",
"git_branch": "RELEASE_3_20",
"git_last_commit": "5c3c2f3",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no",
"Author": "Guangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb]"
},
"DelayedArray": {
"Package": "DelayedArray",
"Version": "0.32.0",
"Source": "Bioconductor",
"Title": "A unified framework for working transparently with on-disk and in-memory array-like datasets",
"Description": "Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.",
"biocViews": "Infrastructure, DataRepresentation, Annotation, GenomeAnnotation",
"URL": "https://bioconductor.org/packages/DelayedArray",
"BugReports": "https://github.com/Bioconductor/DelayedArray/issues",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"Authors@R": "c( person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"), email=\"[email protected]\"), person(\"Aaron\", \"Lun\", role=\"ctb\", email=\"[email protected]\"), person(\"Peter\", \"Hickey\", role=\"ctb\", email=\"[email protected]\"))",
"Maintainer": "Hervé Pagès <[email protected]>",
"Depends": [
"R (>= 4.0.0)",
"methods",
"stats4",
"Matrix",
"BiocGenerics (>= 0.51.3)",
"MatrixGenerics (>= 1.1.3)",
"S4Vectors (>= 0.27.2)",
"IRanges (>= 2.17.3)",
"S4Arrays (>= 1.5.4)",
"SparseArray (>= 1.5.42)"
],
"Imports": [
"stats"
],
"LinkingTo": [
"S4Vectors"
],
"Suggests": [
"BiocParallel",
"HDF5Array (>= 1.17.12)",
"genefilter",
"SummarizedExperiment",
"airway",
"lobstr",
"DelayedMatrixStats",
"knitr",
"rmarkdown",
"BiocStyle",
"RUnit"
],
"VignetteBuilder": "knitr",
"Collate": "compress_atomic_vector.R SparseArraySeed-class.R SparseArraySeed-utils.R read_sparse_block.R makeCappedVolumeBox.R AutoBlock-global-settings.R AutoGrid.R blockApply.R DelayedOp-class.R DelayedSubset-class.R DelayedAperm-class.R DelayedUnaryIsoOpStack-class.R DelayedUnaryIsoOpWithArgs-class.R DelayedSubassign-class.R DelayedSetDimnames-class.R DelayedNaryIsoOp-class.R DelayedAbind-class.R showtree.R simplify.R DelayedArray-class.R DelayedArray-subsetting.R chunkGrid.R RealizationSink-class.R realize.R DelayedArray-utils.R DelayedArray-stats.R matrixStats-methods.R DelayedMatrix-rowsum.R DelayedMatrix-mult.R ConstantArray-class.R RleArraySeed-class.R RleArray-class.R compat.R zzz.R",
"git_url": "https://git.bioconductor.org/packages/DelayedArray",
"git_branch": "RELEASE_3_20",
"git_last_commit": "980c34e",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "yes",
"Author": "Hervé Pagès [aut, cre], Aaron Lun [ctb], Peter Hickey [ctb]"
},
"ExPosition": {
"Package": "ExPosition",
"Version": "2.8.23",
"Source": "Repository",
"Type": "Package",
"Title": "Exploratory Analysis with the Singular Value Decomposition",
"Date": "2018-12-27",
"Author": "Derek Beaton, Cherise R. Chin Fatt, Herve Abdi",
"Maintainer": "Derek Beaton <[email protected]>",
"Description": "A variety of descriptive multivariate analyses with the singular value decomposition, such as principal components analysis, correspondence analysis, and multidimensional scaling. See An ExPosition of the Singular Value Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.",
"License": "GPL-2",
"Depends": [
"prettyGraphs (>= 2.1.4)"
],
"BugReports": "https://github.com/derekbeaton/ExPosition-Family_OLD",
"NeedsCompilation": "no",
"Repository": "CRAN",
"Encoding": "UTF-8"
},
"GO.db": {
"Package": "GO.db",
"Version": "3.20.0",
"Source": "Bioconductor",
"Title": "A set of annotation maps describing the entire Gene Ontology",
"Description": "A set of annotation maps describing the entire Gene Ontology assembled using data from GO",
"Author": "Marc Carlson",
"Maintainer": "Bioconductor Package Maintainer <[email protected]>",
"Depends": [
"R (>= 2.7.0)",
"methods",
"AnnotationDbi (>= 1.67.0)"
],
"Suggests": [
"DBI"
],
"License": "Artistic-2.0",
"biocViews": "AnnotationData, FunctionalAnnotation",
"NeedsCompilation": "no"
},
"GOSemSim": {
"Package": "GOSemSim",
"Version": "2.32.0",
"Source": "Bioconductor",
"Type": "Package",
"Title": "GO-terms Semantic Similarity Measures",
"Authors@R": "c( person(given = \"Guangchuang\", family = \"Yu\", email = \"[email protected]\", role = c(\"aut\", \"cre\")), person(given = \"Alexey\", family = \"Stukalov\", email = \"[email protected]\", role = \"ctb\"), person(given= \"Pingfan\", family = \"Guo\", email = \"[email protected]\", role = \"ctb\"), person(given = \"Chuanle\", family = \"Xiao\", email = \"[email protected]\", role = \"ctb\"), person(given = \"Lluís\", family = \"Revilla Sancho\", email = \"[email protected]\", role = \"ctb\") )",
"Maintainer": "Guangchuang Yu <[email protected]>",
"Description": "The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.",
"Depends": [
"R (>= 3.5.0)"
],
"LinkingTo": [
"Rcpp"
],
"Imports": [
"AnnotationDbi",
"DBI",
"digest",
"GO.db",
"methods",
"rlang",
"R.utils",
"stats",
"utils",
"yulab.utils (>= 0.1.6)"
],
"Suggests": [
"AnnotationHub",
"BiocManager",
"clusterProfiler",
"DOSE",
"knitr",
"org.Hs.eg.db",
"prettydoc",
"rappdirs",
"readr",
"rmarkdown",
"testthat",
"tidyr",
"tidyselect",
"ROCR"
],
"VignetteBuilder": "knitr",
"ByteCompile": "true",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"URL": "https://yulab-smu.top/biomedical-knowledge-mining-book/",
"BugReports": "https://github.com/YuLab-SMU/GOSemSim/issues",
"biocViews": "Annotation, GO, Clustering, Pathways, Network, Software",
"RoxygenNote": "7.3.2",
"git_url": "https://git.bioconductor.org/packages/GOSemSim",
"git_branch": "RELEASE_3_20",
"git_last_commit": "1b53196",
"git_last_commit_date": "2024-10-29",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "yes",
"Author": "Guangchuang Yu [aut, cre], Alexey Stukalov [ctb], Pingfan Guo [ctb], Chuanle Xiao [ctb], Lluís Revilla Sancho [ctb]"
},
"GenomeInfoDb": {
"Package": "GenomeInfoDb",
"Version": "1.42.3",
"Source": "Bioconductor",
"Title": "Utilities for manipulating chromosome names, including modifying them to follow a particular naming style",
"Description": "Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., \"chr1\" versus \"1\"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.",
"biocViews": "Genetics, DataRepresentation, Annotation, GenomeAnnotation",
"URL": "https://bioconductor.org/packages/GenomeInfoDb",
"Video": "http://youtu.be/wdEjCYSXa7w",
"BugReports": "https://github.com/Bioconductor/GenomeInfoDb/issues",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"Authors@R": "c( person(\"Sonali\", \"Arora\", role=\"aut\"), person(\"Martin\", \"Morgan\", role=\"aut\"), person(\"Marc\", \"Carlson\", role=\"aut\"), person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"), email=\"[email protected]\"), person(\"Prisca Chidimma\", \"Maduka\", role=\"ctb\"), person(\"Atuhurira Kirabo\", \"Kakopo\", role=\"ctb\"), person(\"Haleema\", \"Khan\", role=\"ctb\", comment=\"vignette translation from Sweave to Rmarkdown / HTML\"), person(\"Emmanuel Chigozie\", \"Elendu\", role=\"ctb\"))",
"Depends": [
"R (>= 4.0.0)",
"methods",
"BiocGenerics (>= 0.37.0)",
"S4Vectors (>= 0.25.12)",
"IRanges (>= 2.13.12)"
],
"Imports": [
"stats",
"stats4",
"utils",
"UCSC.utils",
"GenomeInfoDbData"
],
"Suggests": [
"R.utils",
"data.table",
"GenomicRanges",
"Rsamtools",
"GenomicAlignments",
"GenomicFeatures",
"BSgenome",
"TxDb.Dmelanogaster.UCSC.dm3.ensGene",
"BSgenome.Scerevisiae.UCSC.sacCer2",
"BSgenome.Celegans.UCSC.ce2",
"BSgenome.Hsapiens.NCBI.GRCh38",
"RUnit",
"BiocStyle",
"knitr"
],
"VignetteBuilder": "knitr",
"Collate": "utils.R fetch_table_dump_from_Ensembl_FTP.R list_ftp_dir.R rankSeqlevels.R NCBI-utils.R UCSC-utils.R Ensembl-utils.R getChromInfoFromNCBI.R getChromInfoFromUCSC.R getChromInfoFromEnsembl.R loadTaxonomyDb.R mapGenomeBuilds.R seqinfo.R Seqinfo-class.R seqlevelsStyle.R seqlevels-wrappers.R GenomeDescription-class.R zzz.R",
"git_url": "https://git.bioconductor.org/packages/GenomeInfoDb",
"git_branch": "RELEASE_3_20",
"git_last_commit": "2f182bf",
"git_last_commit_date": "2025-01-23",
"Repository": "Bioconductor 3.20",
"NeedsCompilation": "no",
"Author": "Sonali Arora [aut], Martin Morgan [aut], Marc Carlson [aut], Hervé Pagès [aut, cre], Prisca Chidimma Maduka [ctb], Atuhurira Kirabo Kakopo [ctb], Haleema Khan [ctb] (vignette translation from Sweave to Rmarkdown / HTML), Emmanuel Chigozie Elendu [ctb]",
"Maintainer": "Hervé Pagès <[email protected]>"
},
"GenomeInfoDbData": {
"Package": "GenomeInfoDbData",
"Version": "1.2.13",
"Source": "Bioconductor",
"Title": "Species and taxonomy ID look up tables used by GenomeInfoDb",
"Description": "Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.",
"Author": "Bioconductor Core Team",
"Maintainer": "Bioconductor Maintainer <[email protected]>",
"Depends": [
"R (>= 3.5.0)"
],
"biocViews": "AnnotationData, Organism",
"License": "Artistic-2.0",
"NeedsCompilation": "no"
},
"GenomicAlignments": {
"Package": "GenomicAlignments",
"Version": "1.42.0",
"Source": "Bioconductor",
"Title": "Representation and manipulation of short genomic alignments",
"Description": "Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.",
"biocViews": "Infrastructure, DataImport, Genetics, Sequencing, RNASeq, SNP, Coverage, Alignment, ImmunoOncology",
"URL": "https://bioconductor.org/packages/GenomicAlignments",
"Video": "https://www.youtube.com/watch?v=2KqBSbkfhRo , https://www.youtube.com/watch?v=3PK_jx44QTs",
"BugReports": "https://github.com/Bioconductor/GenomicAlignments/issues",
"License": "Artistic-2.0",
"Encoding": "UTF-8",
"Authors@R": "c( person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"), email=\"[email protected]\"), person(\"Valerie\", \"Obenchain\", role=\"aut\"), person(\"Martin\", \"Morgan\", role=\"aut\"), person(\"Fedor\", \"Bezrukov\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Halimat C.\", \"Atanda\", role=\"ctb\", comment=\"Translated 'WorkingWithAlignedNucleotides' vignette from Sweave to RMarkdown / HTML.\" ))",
"Depends": [
"R (>= 4.0.0)",
"methods",
"BiocGenerics (>= 0.37.0)",
"S4Vectors (>= 0.27.12)",
"IRanges (>= 2.23.9)",
"GenomeInfoDb (>= 1.13.1)",
"GenomicRanges (>= 1.55.3)",
"SummarizedExperiment (>= 1.9.13)",
"Biostrings (>= 2.55.7)",
"Rsamtools (>= 1.31.2)"
],
"Imports": [
"methods",
"utils",
"stats",
"BiocGenerics",
"S4Vectors",
"IRanges",
"GenomicRanges",
"Biostrings",
"Rsamtools",
"BiocParallel"
],
"LinkingTo": [
"S4Vectors",
"IRanges"
],
"Suggests": [
"ShortRead",
"rtracklayer",
"BSgenome",
"GenomicFeatures",
"RNAseqData.HNRNPC.bam.chr14",
"pasillaBamSubset",
"TxDb.Hsapiens.UCSC.hg19.knownGene",
"TxDb.Dmelanogaster.UCSC.dm3.ensGene",
"BSgenome.Dmelanogaster.UCSC.dm3",
"BSgenome.Hsapiens.UCSC.hg19",
"DESeq2",
"edgeR",
"RUnit",
"knitr",
"BiocStyle"
],
"Collate": "utils.R cigar-utils.R GAlignments-class.R GAlignmentPairs-class.R GAlignmentsList-class.R GappedReads-class.R OverlapEncodings-class.R findMateAlignment.R readGAlignments.R junctions-methods.R sequenceLayer.R pileLettersAt.R stackStringsFromGAlignments.R intra-range-methods.R coverage-methods.R setops-methods.R findOverlaps-methods.R coordinate-mapping-methods.R encodeOverlaps-methods.R findCompatibleOverlaps-methods.R summarizeOverlaps-methods.R findSpliceOverlaps-methods.R zzz.R",
"VignetteBuilder": "knitr",
"git_url": "https://git.bioconductor.org/packages/GenomicAlignments",