ydeng/bch441-work-abc-units
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  • 76b18a8a35 Update PPI-Analysis assets and code hyginn 2020-09-23 20:47:26 +10:00
  • 42ad74b2f2 Changed 1 to 3 hyginn 2020-09-23 14:13:52 +10:00
  • cf90c52a61 Update the ScCC network data hyginn 2020-09-23 14:06:58 +10:00
  • 02e20ba812 Maintenance hyginn 2020-09-23 13:00:38 +10:00
  • 0e71fc337e Maintenance and sample solutions hyginn 2020-09-23 06:07:40 +10:00
  • 4c0e75d792 Maintenance hyginn 2020-09-23 00:32:36 +10:00
  • f90f581963 ToDo ... hyginn 2020-09-22 21:02:27 +10:00
  • 4c2e911a5a 2020 Maintenance hyginn 2020-09-22 21:02:13 +10:00
  • ca0d78c4b9 stylisitc updates hyginn 2020-09-22 13:02:29 +10:00
  • 67c92a49d9 change validation logic in selectPDBrep() and add seal() hyginn 2020-09-22 13:02:10 +10:00
  • 03674b57dc set to active and update submission tasks hyginn 2020-09-21 21:35:16 +10:00
  • cfbfee9dba add digest:: and jsonlite::, and sameSpecies(), hyginn 2020-09-21 21:34:45 +10:00
  • b1d712891f Set to active, and tweak subtitle hyginn 2020-09-21 15:23:27 +10:00
  • 12c11a6351 Update plot and legend layout hyginn 2020-09-21 15:06:27 +10:00
  • 2432d64f18 update process for moving .myProfile.R hyginn 2020-09-21 14:54:30 +10:00
  • 3082b05a0b Moved setting default stringsAsFactors to .myProfile.R since it needs to persist hyginn 2020-09-21 14:44:08 +10:00
  • 61a2c01be4 add options(stringsAsFactors = FALSE) as comment - if needed hyginn 2020-09-21 14:40:04 +10:00
  • 7536473c5d Updated MYSPE data and entire workflow. Changed all .RData to .rds hyginn 2020-09-21 14:28:24 +10:00
  • 3d91337e70 New workflow for Introduction hyginn 2020-09-19 22:31:06 +10:00
  • 37ef655d47 2020 updates - deactivate for maintenance hyginn 2020-09-18 21:56:30 +10:00
  • 89bdd14d1c Test for default stringsAsFactors and complain if TRUE hyginn 2020-09-18 08:48:19 +10:00
  • 599f8a3f98 2020 updates and maintenance hyginn 2020-09-16 16:32:51 +10:00
  • 46a157bb17 Maintenance hyginn 2019-11-14 22:44:07 -05:00
  • 5b197b8829 Maintenance hyginn 2019-11-14 22:40:45 -05:00
  • bae2d33f14 Prefix Biostrings:: to subseq() hyginn 2019-11-14 22:38:53 -05:00
  • 84aa2dca0b prefix function with package name hyginn 2019-11-14 22:12:33 -05:00
  • cffd803c23 Use requireNamespace(), <package>::<function>() idiom, Biocmanager:: - not biocLite() hyginn 2019-01-08 17:11:25 +10:00
  • 8cdbb9f4cc myScript.R should not exist in master hyginn 2019-01-08 11:32:39 +10:00
  • c7393ca287 cleanup hyginn 2019-01-07 17:51:50 +10:00
  • 64772c5702 sample data hyginn 2019-01-07 17:51:11 +10:00
  • 6f54293592 Maintenance updates, and revised set.seed() usage hyginn 2019-01-07 16:17:23 +10:00
  • 2ab162e375 Maintance: typos, update of prosite URL hyginn 2018-12-02 18:52:36 +10:00
  • 1dd87e7473 Maintainance fixes and UniProt API change bugfix hyginn 2018-10-30 21:27:42 -04:00
  • ead20d5f18 Fixed merge conflict noise hyginn 2018-01-28 18:53:10 -05:00
  • c17b340b38 Add material hyginn 2018-01-28 18:49:24 -05:00
  • c4fed71a7f Add section on GPL annotations to RPR-GEO2R hyginn 2018-01-28 18:23:21 -05:00
  • b17a9e202a Add section on GPL annotations to RPR-GEO2R hyginn 2018-01-28 18:23:21 -05:00
  • 359434d863 Typo hyginn 2017-11-23 07:19:31 -05:00
  • 75c6efe4a6 variable name typo hyginn 2017-11-23 00:32:13 -05:00
  • 8ac1582514 TRUE and FALSE were inverted in explanation of masking hyginn 2017-11-22 12:05:02 -05:00
  • 5e4ecbaf6f New code - under development hyginn 2017-11-20 19:01:20 -05:00
  • 82841de74a Change blockWidth > 60 from error to warning hyginn 2017-11-20 19:00:55 -05:00
  • a1b5eb7b90 Correction re. Jeffreys' pseudocounts hyginn 2017-11-20 19:00:23 -05:00
  • 9a987c22be Add comment re. failing msaMuscle() hyginn 2017-11-20 18:59:54 -05:00
  • f747f7896e typo hyginn 2017-11-17 23:44:05 -05:00
  • 450aefa119 New unit hyginn 2017-11-17 23:43:50 -05:00
  • 40b9e6fc04 update to function <- package::function idiom hyginn 2017-11-16 16:37:53 -05:00
  • 62a1a76558 Updated logic hyginn 2017-11-16 16:01:56 -05:00
  • 4bbf663eca load seqinr hyginn 2017-11-16 14:46:15 -05:00
  • a58e35f060 Fixed parsing and added missing logic hyginn 2017-11-16 11:47:53 -05:00
  • 206e2e14bb New unit, and update to annotation file logic hyginn 2017-11-14 02:57:13 -05:00
  • 2433bc8652 fixed annotation errors hyginn 2017-11-14 02:56:39 -05:00
  • 8cb69f2986 New unit hyginn 2017-11-13 00:51:04 -05:00
  • 93523c6533 New unit and associated data hyginn 2017-11-12 04:39:00 -05:00
  • 28be433b83 Added ToDo hyginn 2017-11-12 04:38:15 -05:00
  • c93b6df235 Style hyginn 2017-11-12 04:37:53 -05:00
  • 16d96d79f4 New unit and data hyginn 2017-11-09 23:44:25 -05:00
  • 943dbeba8f style fix hyginn 2017-11-09 23:43:48 -05:00
  • f1e222f4e0 Bugfixes hyginn 2017-11-03 15:20:16 -04:00
  • 2b6ca615b9 Merge branch 'master' of https://github.com/hyginn/ABC-units hyginn 2017-11-03 15:19:14 -04:00
  • 67abde8920 bugfix hyginn 2017-11-03 15:08:17 -04:00
  • 563ae186d0 bugfix hyginn 2017-11-03 15:08:17 -04:00
  • 1d6170f417 Updates, and add treedist() hyginn 2017-11-01 23:30:01 -04:00
  • 0da30ec109 bugfix hyginn 2017-11-01 23:29:30 -04:00
  • 6121323df3 Correct calculation of empirical p-vale hyginn 2017-11-01 23:29:18 -04:00
  • f6983b142a Update hyginn 2017-11-01 23:28:12 -04:00
  • 8fe794cf33 add PHYLO units hyginn 2017-11-01 09:44:24 -04:00
  • 7cc2853d00 add fetchMSAmotif() function hyginn 2017-11-01 09:43:32 -04:00
  • d3c42da51b bugfix (old code carryover) hyginn 2017-10-30 17:24:09 -04:00
  • 373da689df bugfixes hyginn 2017-10-29 22:19:19 -04:00
  • 553b042f20 MSA unit, and supporting files hyginn 2017-10-28 23:09:21 -04:00
  • 044990d1c9 coding style: hyginn 2017-10-28 23:08:31 -04:00
  • 066be49970 added a non-executing block for test code hyginn 2017-10-28 23:07:52 -04:00
  • 4479fa2d4d Added package information code after every library() call. hyginn 2017-10-28 23:05:53 -04:00
  • e57db9e9a0 Added data files for PSI-BLAST unit, updated some other JSONs hyginn 2017-10-23 21:00:39 -04:00
  • bc4afc97aa Updates for BIN-ALI-BLAST hyginn 2017-10-23 12:37:09 -04:00
  • 59ab6c573f New unit and associated FASTA files hyginn 2017-10-22 23:39:12 -04:00
  • 932c81c8d1 New unit hyginn 2017-10-22 23:38:32 -04:00
  • 50bf936bd5 Data for RPR-SX-PDB unit hyginn 2017-10-21 21:02:13 -04:00
  • 483386bf3b Live version of RPR-SX-PDB.R hyginn 2017-10-21 21:01:29 -04:00
  • 46285224d6 New unit RPR-Biostrings.R hyginn 2017-10-21 21:00:55 -04:00
  • b748c1264c Add selectPDBrep() function to select random, representative PDB IDs hyginn 2017-10-21 21:00:18 -04:00
  • d28536b395 Data files for ABC-INT-Mutation_impact integrator unit hyginn 2017-10-17 07:32:01 -04:00
  • a942bef91e New unit hyginn 2017-10-15 23:40:13 -04:00
  • 05958349cf New unit: RPR-Unit_tests, with sample test file and tests directory hyginn 2017-10-15 18:46:42 -04:00
  • c148d95071 updates to biCode() function - handle NA and short input hyginn 2017-10-15 18:44:06 -04:00
  • 153e7dcf00 Update: FASTA files may contain gap and stop characters hyginn 2017-10-14 18:26:16 -04:00
  • d9e7813d27 Code and data for RPR-FASTA hyginn 2017-10-14 18:25:46 -04:00
  • edb245f818 Comments on "incomplete final line" warning hyginn 2017-10-12 21:50:30 -04:00
  • bd79626a3d clarifications hyginn 2017-10-12 15:14:46 -04:00
  • 98cd17bfe0 New unit code hyginn 2017-10-12 15:11:38 -04:00
  • 0c069a66ca add ID mapping instructions hyginn 2017-10-09 17:32:07 -04:00
  • 32a45fc059 Add UniProtIDmap() function hyginn 2017-10-08 15:59:56 -04:00
  • 59a1341796 New unit hyginn 2017-10-08 15:59:36 -04:00
  • 96e559429d S. cerevisae cell cycle subnetwork edge-list hyginn 2017-10-07 13:57:55 -04:00
  • 7ed5309901 Supporting script to create a cell cycle subset from STRING data. Used for FND-MAT-Graphs_and_networks deliverables hyginn 2017-10-07 11:52:33 -04:00
  • f2e1f4ca83 First live version hyginn 2017-10-07 11:51:08 -04:00
  • 27dd73664b add httr and xml2 package, add scripted data download functions hyginn 2017-10-06 08:51:12 -04:00
  • b33feed50a Add code for scripting data download unit hyginn 2017-10-06 08:49:43 -04:00
  • 4fb2506e58 refactor biCode to bring it in line with current coding standards hyginn 2017-10-06 08:49:10 -04:00