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gidb_dev

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#1

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• 0bb81f6566 Update README.md master tanu 2023-11-27 15:12:37 +00:00
• 32cd353e12 Update README.md tanu 2023-11-27 15:11:46 +00:00
• 1c616eeb71 bugfixes Tanushree Tunstall 2023-02-27 20:02:10 +00:00
• a405cd8035 add consurf-only scripts Tanushree Tunstall 2023-02-25 17:08:22 +00:00
• 9bc18169cf tweaks to thesis figs Tanushree Tunstall 2023-02-24 22:38:37 +00:00
• e9d841d989 table generator Tanushree Tunstall 2023-02-23 21:04:58 +00:00
• c2d6eb49ea figure fixup Tanushree Tunstall 2023-02-21 21:01:00 +00:00
• c1441dc0d6 import thesis plots from Misc Tanushree Tunstall 2023-02-21 20:41:59 +00:00
• 1571f430a5 fix HARDCODED HOMEDIRS Tanushree Tunstall 2023-02-19 18:01:03 +00:00
• db7e2912e1 SNP -> SAV for thesis plots Tanushree Tunstall 2023-02-19 17:43:22 +00:00
• 777d3765cf a bunch of small changes Tanushree Tunstall 2023-02-19 17:22:15 +00:00
• 4640f9024a remove empty LF files Tanushree Tunstall 2022-10-11 14:19:39 +01:00
• ca73bc9b48 lf_bp2: extend y Tanushree Tunstall 2022-10-11 12:04:55 +01:00
• a74f11ce79 lf_bp2: extend y Tanushree Tunstall 2022-10-11 12:03:45 +01:00
• 39fe2da8be lf_bp2: extend y Tanushree Tunstall 2022-10-11 12:01:46 +01:00
• 763ffa55b8 lf_bp2: extend y Tanushree Tunstall 2022-10-11 11:56:41 +01:00
• 5966c4e21b lf_bp2: extend y Tanushree Tunstall 2022-10-11 11:53:17 +01:00
• 37e970dea3 lf_bp2: extend y axis Tanushree Tunstall 2022-10-11 11:51:20 +01:00
• 25cfe39c71 saving Tanushree Tunstall 2022-09-14 17:11:39 +01:00
• 4f01695391 site_snp_count_bp error handler Tanushree Tunstall 2022-09-09 19:37:38 +01:00
• 0a4be280c3 various bugfixes Tanushree Tunstall 2022-09-07 20:03:43 +01:00
• 590cec5e99 added pnca plots Tanushree Tunstall 2022-09-06 21:36:28 +01:00
• ade1739753 saving Tanushree Tunstall 2022-09-06 21:35:59 +01:00
• 23bb087ea3 plot function fixes for position tiles Tanushree Tunstall 2022-09-06 17:06:01 +01:00
• 07826fbc91 alr: remove 113 Tanushree Tunstall 2022-09-05 19:32:36 +01:00
• bb022470d9 stuff Tanushree Tunstall 2022-09-05 19:27:11 +01:00
• 4a34d7a94d alr config Tanushree Tunstall 2022-09-05 19:03:49 +01:00
• f1f0d3e62e alr config Tanushree Tunstall 2022-09-05 19:00:09 +01:00
• e9fb582db9 msa indexes Tanushree Tunstall 2022-09-05 18:49:40 +01:00
• 1241ad0b22 various usability tweaks to LogoPlotMSA and position_annotation Tanushree Tunstall 2022-09-05 16:05:45 +01:00
• f949592dd8 added consurf_colours_no_isd to ensure consurf plots are not messed up in the absesnce of 0 categ Tanushree Tunstall 2022-09-05 16:01:21 +01:00
• 2cec743ae0 added pnca plot dir to generate plots that weren#t covered in the paper Tanushree Tunstall 2022-09-05 14:02:04 +01:00
• 1dacebbaf6 renamed files for lineage_diff_sensitivites.R Tanushree Tunstall 2022-09-05 13:19:06 +01:00
• 69a0da0a59 added script for lineage diff sensitivities Tanushree Tunstall 2022-09-04 21:36:49 +01:00
• 4963f18f1d added 113 to alr aa Tanushree Tunstall 2022-09-04 21:36:14 +01:00
• 58c25e23c0 added ml_iterator.py Tanushree Tunstall 2022-09-03 14:42:13 +01:00
• 4976e9d8af saving Tanushree Tunstall 2022-09-03 14:41:22 +01:00
• 2b953583e2 added combined model FS code and run script Tanushree Tunstall 2022-09-03 12:28:36 +01:00
• 78704dec5a saving Tanushree Tunstall 2022-09-03 12:28:21 +01:00
• 889bea1e63 ran ml_iterator for actual genes Tanushree Tunstall 2022-09-03 09:23:14 +01:00
• d77389acfc running combined model with FS Tanushree Tunstall 2022-09-03 09:21:34 +01:00
• c7351970a2 chmod Tanushree Tunstall 2022-09-02 21:14:02 +01:00
• f9ce90e3f4 saving Tanushree Tunstall 2022-09-02 10:08:58 +01:00
• 93e958ae6a now running for combined gene actual Tanushree Tunstall 2022-09-02 10:04:27 +01:00
• 00ca7a6b27 tweaks Tanushree Tunstall 2022-09-02 09:49:06 +01:00
• c845d96102 added combined_model_iterator.py that has oversampling Tanushree Tunstall 2022-09-02 09:50:51 +01:00
• 338dd329e9 running ml_iterator_CV for all targets with different CV threholds Tanushree Tunstall 2022-09-01 16:29:32 +01:00
• 80b4a1850c tested to make sure the cols added dont break code Tanushree Tunstall 2022-09-01 16:23:57 +01:00
• de9e6a709b added 3 cols for snp counts for ML Tanushree Tunstall 2022-09-01 16:11:23 +01:00
• 2bf91681b4 preparing to rerun ML iterator Tanushree Tunstall 2022-09-01 13:41:02 +01:00
• 56b71c6ca2 added avg affinity and stability cols with mask for avg affinity Tanushree Tunstall 2022-09-01 13:04:37 +01:00
• e03ce277b7 checked masked cols after running Tanushree Tunstall 2022-09-01 12:57:38 +01:00
• f9129b9ebc added nca dist criteria for masking Tanushree Tunstall 2022-09-01 12:55:38 +01:00
• f94eadf1d4 added Tanushree Tunstall 2022-09-01 12:54:41 +01:00
• 82e2da4f3b ml df stuff Tanushree Tunstall 2022-09-01 11:39:11 +01:00
• c2b46286d8 added rpob ks test script Tanushree Tunstall 2022-08-31 22:03:39 +01:00
• bc9d1a7149 added embb plotting scripts Tanushree Tunstall 2022-08-31 22:03:07 +01:00
• a5d22540e1 renamed count_vars_ML previous version as such Tanushree Tunstall 2022-08-31 22:02:16 +01:00
• 14e655eeeb gid correction Tanushree Tunstall 2022-08-30 12:11:43 +01:00
• 317b97bc9c stuff Tanushree Tunstall 2022-08-30 12:10:49 +01:00
• d7f348318c removed template files from rpob Tanushree Tunstall 2022-08-29 23:28:53 +01:00
• f39bbdcce7 added katg and rpob files Tanushree Tunstall 2022-08-29 23:27:37 +01:00
• 7c2e4b898e added rpob plot scripts Tanushree Tunstall 2022-08-29 23:26:43 +01:00
• 8f97ab7cc8 rpob Tanushree Tunstall 2022-08-29 18:23:43 +01:00
• 6441be21ab added katg tables Tanushree Tunstall 2022-08-28 22:31:12 +01:00
• d5da923a74 stuff Tanushree Tunstall 2022-08-28 13:16:46 +01:00
• 7bed6a1e22 added all scripts Tanushree Tunstall 2022-08-27 23:12:00 +01:00
• da8a1069a8 saving work Tanushree Tunstall 2022-08-27 23:11:44 +01:00
• c3067b9176 gg pairs fixup for alr Tanushree Tunstall 2022-08-27 17:15:31 +01:00
• 5b89beb2b5 readded removed positions in alr Tanushree Tunstall 2022-08-27 17:07:08 +01:00
• 927ab850a8 added DCS to alr config Tanushree Tunstall 2022-08-27 16:36:35 +01:00
• c6f5a446c3 stuff Tanushree Tunstall 2022-08-27 15:35:41 +01:00
• 79b251047d allow position_annotation to specify colours Tanushree Tunstall 2022-08-25 19:09:56 +01:00
• 2cbc460f87 added output tables with active site Tanushree Tunstall 2022-08-26 21:50:33 +01:00
• f290d8ec9e addded appendix tables and frequent muts Tanushree Tunstall 2022-08-25 22:21:05 +01:00
• 741aad3dd1 added nsSNPs to lineage dist plots Tanushree Tunstall 2022-08-25 22:17:20 +01:00
• ca619bc662 fix directory assumption Tanushree Tunstall 2022-08-25 18:02:25 +01:00
• afa9166ca8 things Tanushree Tunstall 2022-08-25 17:57:58 +01:00
• cd76a4b919 things Tanushree Tunstall 2022-08-25 11:54:40 +01:00
• 3b77b4b611 stuff Tanushree Tunstall 2022-08-24 16:52:11 +01:00
• e4e8bd7278 added colors for tiles for gid plots and appendix tables Tanushree Tunstall 2022-08-25 17:50:49 +01:00
• ac72634b48 added dir for embb for consistency and checks and moved others to version1 Tanushree Tunstall 2022-08-25 10:19:25 +01:00
• 19b820e316 corrected the pe colour mapping Tanushree Tunstall 2022-08-24 20:55:36 +01:00
• 11b936f09b added more scripts Tanushree Tunstall 2022-08-24 20:04:29 +01:00
• 9aed99e805 various Tanushree Tunstall 2022-08-23 21:54:16 +01:00
• 0284122ef2 aadded replace bfactor for na Tanushree Tunstall 2022-08-23 16:31:17 +01:00
• 23b4f06017 added scripts Tanushree Tunstall 2022-08-23 16:30:42 +01:00
• dd69da01f6 get_plotting_dfs Tanushree Tunstall 2022-08-23 15:19:36 +01:00
• ee70845939 stuff Tanushree Tunstall 2022-08-22 11:43:45 +01:00
• a2e7e6c26b plerts Tanushree Tunstall 2022-08-22 23:11:42 +01:00
• 3d817fde0c more plot files Tanushree Tunstall 2022-08-22 22:57:56 +01:00
• 04253b961f lots of per-plot configs Tanushree Tunstall 2022-08-22 21:56:13 +01:00
• 13999a477d fixed source to contain plotting cols and pos_count correctly Tanushree Tunstall 2022-08-22 14:33:06 +01:00
• 4147a6b90f a massive waste of time Tanushree Tunstall 2022-08-22 13:05:53 +01:00
• 8d6c148fff renamed 2 to _v2 Tanushree Tunstall 2022-08-22 10:53:25 +01:00
• 802d6f8495 renamed 2 to _v2 Tanushree Tunstall 2022-08-22 11:41:42 +01:00
• c9d7ea9fad AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA Tanushree Tunstall 2022-08-17 18:42:15 +01:00
• cd9b1ad245 stability and cons revised bp out Tanushree Tunstall 2022-08-16 14:45:31 +01:00
• f244741e83 added Lin_count.R Tanushree Tunstall 2022-08-15 21:29:16 +01:00
• 2e29cf8011 config files Tanushree Tunstall 2022-08-15 20:39:35 +01:00