Commit Graph

33 Commits

Author SHA1 Message Date
hyginn
33ba40a252 Bugfix in AddProtein - paste() returns deparsed expression for single-column lists... 2020-11-09 22:02:27 +10:00
hyginn
55a0d18a66 patch a problem where jsonlite:: oversimplifies from single entries to array, rather than list. 2020-10-13 22:38:47 +10:00
hyginn
5524832a75 bugfix: wrong iterator 2020-10-13 21:45:14 +10:00
hyginn
a50688e0d0 bugfix: jsonlite::fromJSON() chokes on a blank 2020-10-13 20:35:45 +10:00
hyginn
804e3a73b7 bugfix: import all taxonomy IDs as integer 2020-10-13 20:33:04 +10:00
hyginn
0541612e0b Bugfixes 2020-10-13 20:27:56 +10:00
hyginn
4d071cf8d5 Add code and utility functions for database export of protein annotations to JSON - towards sharing annotations on the Student Wiki Public page 2020-10-13 16:08:35 +10:00
hyginn
169ca58b92 Bugfix: q -> Q 2020-09-25 21:51:04 +10:00
hyginn
abb146f828 bugfix in dbFetchPrositeFeatures(); add return of actual motif sequence; stylistic updates 2020-09-25 11:29:28 +10:00
hyginn
36140bc984 updates; vectorized dbFetchUniProtSeq() 2020-09-25 10:47:41 +10:00
hyginn
2775c7c9a8 Updates to UniProtIDmap, and address httr/curl initialization bug 2020-09-25 02:27:42 +10:00
hyginn
76b18a8a35 Update PPI-Analysis assets and code 2020-09-23 20:47:26 +10:00
hyginn
cf90c52a61 Update the ScCC network data 2020-09-23 14:06:58 +10:00
hyginn
f90f581963 ToDo ... 2020-09-22 21:02:27 +10:00
hyginn
7536473c5d Updated MYSPE data and entire workflow. Changed all .RData to .rds 2020-09-21 14:28:24 +10:00
hyginn
37ef655d47 2020 updates - deactivate for maintenance 2020-09-18 21:56:30 +10:00
hyginn
84aa2dca0b prefix function with package name 2019-11-14 22:12:33 -05:00
hyginn
cffd803c23 Use requireNamespace(), <package>::<function>() idiom,
Biocmanager:: - not biocLite()
2019-01-08 17:11:25 +10:00
hyginn
2ab162e375 Maintance: typos, update of prosite URL 2018-12-02 18:52:36 +10:00
hyginn
1dd87e7473 Maintainance fixes and UniProt API change bugfix 2018-10-30 21:27:42 -04:00
hyginn
82841de74a Change blockWidth > 60 from error to warning 2017-11-20 19:00:55 -05:00
hyginn
a58e35f060 Fixed parsing and added missing logic 2017-11-16 11:47:53 -05:00
hyginn
0da30ec109 bugfix 2017-11-01 23:29:30 -04:00
hyginn
553b042f20 MSA unit, and supporting files 2017-10-28 23:09:21 -04:00
hyginn
044990d1c9 coding style: 2017-10-28 23:08:31 -04:00
hyginn
e57db9e9a0 Added data files for PSI-BLAST unit, updated some other JSONs 2017-10-23 21:00:39 -04:00
hyginn
bc4afc97aa Updates for BIN-ALI-BLAST 2017-10-23 12:37:09 -04:00
hyginn
153e7dcf00 Update: FASTA files may contain gap and stop characters 2017-10-14 18:26:16 -04:00
hyginn
32a45fc059 Add UniProtIDmap() function 2017-10-08 15:59:56 -04:00
hyginn
7ed5309901 Supporting script to create a cell cycle subset from STRING data. Used for FND-MAT-Graphs_and_networks deliverables 2017-10-07 11:52:33 -04:00
hyginn
27dd73664b add httr and xml2 package, add scripted data download functions 2017-10-06 08:51:12 -04:00
hyginn
e1dbd1d268 update function to remove FASTA headers (line-break terminated substrings that begin with a ">") 2017-09-29 12:25:00 -04:00
hyginn
95accd9608 new scripts 2017-09-25 01:31:40 -04:00