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gidb_dev

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• acda9f13e5 saving the correct af or script Tanushree Tunstall 2021-06-11 13:26:28 +01:00
• 587be435e9 saving the correct af or script Tanushree Tunstall 2021-06-11 13:26:28 +01:00
• e78707067c saving work before converting to a function Tanushree Tunstall 2021-06-11 13:25:02 +01:00
• 4e38e2a80e saving work before converting to a function Tanushree Tunstall 2021-06-11 13:25:02 +01:00
• a2431b59e5 minor tweak to plotting_globals.R to make gene_match a global var Tanushree Tunstall 2021-06-11 11:21:20 +01:00
• d9e00b9a42 minor tweak to plotting_globals.R to make gene_match a global var Tanushree Tunstall 2021-06-11 11:21:20 +01:00
• f6259aa517 moved functions/ in the scripts dir Tanushree Tunstall 2021-06-11 11:11:39 +01:00
• 29fa99b914 moved functions/ in the scripts dir Tanushree Tunstall 2021-06-11 11:11:39 +01:00
• 0c3645705d moved old bp scripts to redundant Tanushree Tunstall 2021-06-10 16:18:08 +01:00
• 2dc81e72f4 moved old bp scripts to redundant Tanushree Tunstall 2021-06-10 16:18:08 +01:00
• dccdfe9742 moved plotting_func to functions and replaced 3 basic_barplots scripts with 1 Tanushree Tunstall 2021-06-10 16:09:58 +01:00
• ff7522eca2 moved plotting_func to functions and replaced 3 basic_barplots scripts with 1 Tanushree Tunstall 2021-06-10 16:09:58 +01:00
• 5c018e23be added function for position_count_bp.R Tanushree Tunstall 2021-06-10 14:46:11 +01:00
• b9d176afa4 added function for position_count_bp.R Tanushree Tunstall 2021-06-10 14:46:11 +01:00
• 4bee48f545 added functions dir for further tidying and tested this with ind scripts for stability Tanushree Tunstall 2021-06-09 18:13:18 +01:00
• cbb3749a21 added functions dir for further tidying and tested this with ind scripts for stability Tanushree Tunstall 2021-06-09 18:13:18 +01:00
• 786eaabe1a moved bp function script to function/ Tanushree Tunstall 2021-06-09 17:08:56 +01:00
• 912a439589 moved bp function script to function/ Tanushree Tunstall 2021-06-09 17:08:56 +01:00
• 225360fb93 added shiny app and turned stability bp to function Tanushree Tunstall 2021-06-09 17:05:02 +01:00
• 826b8aa9d0 added shiny app and turned stability bp to function Tanushree Tunstall 2021-06-09 17:05:02 +01:00
• 3f58a5c64c saving work Tanushree Tunstall 2021-06-09 16:27:05 +01:00
• f871dd39cd saving work Tanushree Tunstall 2021-06-09 16:27:05 +01:00
• 776c4e0279 repuposed and ran basic_barplots for lig and foldx including filenames Tanushree Tunstall 2021-06-09 11:33:08 +01:00
• 47a6ddbf72 repuposed and ran basic_barplots for lig and foldx including filenames Tanushree Tunstall 2021-06-09 11:33:08 +01:00
• d45a9499a2 repurposed basic_barplots_foldx.R Tanushree Tunstall 2021-06-09 11:24:50 +01:00
• 27d79105ef repurposed basic_barplots_foldx.R Tanushree Tunstall 2021-06-09 11:24:50 +01:00
• 6f24fc1fac uddated how to run plotting scripts. This is a cleaner version to keep up-to-date Tanushree Tunstall 2021-06-08 16:53:07 +01:00
• 8f73c7b804 uddated how to run plotting scripts. This is a cleaner version to keep up-to-date Tanushree Tunstall 2021-06-08 16:53:07 +01:00
• ce8abafdfe wrapper script basic_barplots_PS.R now takes cmd and calls functions to generate plots.Tested and verfiied. Tanushree Tunstall 2021-06-08 16:48:19 +01:00
• 3f691281bc wrapper script basic_barplots_PS.R now takes cmd and calls functions to generate plots.Tested and verfiied. Tanushree Tunstall 2021-06-08 16:48:19 +01:00
• b25511a239 tidied plotting_data.R as a function returning a lits of dfs Tanushree Tunstall 2021-06-08 16:00:28 +01:00
• 1505a3c707 tidied plotting_data.R as a function returning a lits of dfs Tanushree Tunstall 2021-06-08 16:00:28 +01:00
• b8d0bc416a added plotting_globals and text file with info on how to run plotting scripst Tanushree Tunstall 2021-06-04 17:26:01 +01:00
• 9af0249e0e added plotting_globals and text file with info on how to run plotting scripst Tanushree Tunstall 2021-06-04 17:26:01 +01:00
• d21605b31f tweaking baic bp to make generic Tanushree Tunstall 2021-06-04 17:23:41 +01:00
• a5715bcccc tweaking baic bp to make generic Tanushree Tunstall 2021-06-04 17:23:41 +01:00
• 4f60e93abb minor updates to dir.R Tanushree Tunstall 2021-06-04 15:05:52 +01:00
• aaa24ca32d minor updates to dir.R Tanushree Tunstall 2021-06-04 15:05:52 +01:00
• 7242b3516b adpated combining_dfs.py and plotting.R for gid and attempting to make it generic Tanushree Tunstall 2021-06-04 14:36:16 +01:00
• a1fef205da adpated combining_dfs.py and plotting.R for gid and attempting to make it generic Tanushree Tunstall 2021-06-04 14:36:16 +01:00
• d52534f676 test branch commit Tanushree Tunstall 2021-06-04 09:43:48 +01:00
• 2c5c704d0b test branch commit Tanushree Tunstall 2021-06-04 09:43:48 +01:00
• 18af246c24 saving before starting work Tanushree Tunstall 2021-06-04 09:38:17 +01:00
• b77f55fcc2 saving before starting work Tanushree Tunstall 2021-06-04 09:38:17 +01:00
• 8009c3fe3d updated counts.py with wt seq counts Tanushree Tunstall 2021-03-03 11:54:48 +00:00
• 59430a49dd updated counts.py with wt seq counts Tanushree Tunstall 2021-03-03 11:54:48 +00:00
• c59e3f178d added adjusted p-values for DM muts comparison Tanushree Tunstall 2021-02-27 10:42:04 +00:00
• 88229860e2 added adjusted p-values for DM muts comparison Tanushree Tunstall 2021-02-27 10:42:04 +00:00
• bbec97b00c updated count.py with indel and stop codon count Tanushree Tunstall 2021-02-24 09:56:36 +00:00
• 9784bc1729 updated count.py with indel and stop codon count Tanushree Tunstall 2021-02-24 09:56:36 +00:00
• 9062751790 retrieved results for gid b8 and b9 Tanushree Tunstall 2021-02-23 08:59:01 +00:00
• 8975a4cedf retrieved results for gid b8 and b9 Tanushree Tunstall 2021-02-23 08:59:01 +00:00
• 77efd0b76d retrieved gid b7 and submitted b8,b9 and b10 Tanushree Tunstall 2021-02-22 09:31:29 +00:00
• 3ec42edc57 retrieved gid b7 and submitted b8,b9 and b10 Tanushree Tunstall 2021-02-22 09:31:29 +00:00
• 88dad2696f retrieved results for gid b6 Tanushree Tunstall 2021-02-21 16:23:22 +00:00
• 7925a408cd retrieved results for gid b6 Tanushree Tunstall 2021-02-21 16:23:22 +00:00
• 34c0b808ea added count.py to count samples for quick checks Tanushree Tunstall 2021-02-21 16:07:33 +00:00
• aca73048c1 added count.py to count samples for quick checks Tanushree Tunstall 2021-02-21 16:07:33 +00:00
• 05562399ce saving work and generating revised_figure7 Tanushree Tunstall 2021-02-20 16:17:38 +00:00
• 9b0d2f6550 saving work and generating revised_figure7 Tanushree Tunstall 2021-02-20 16:17:38 +00:00
• 9f03e6a6fd dynamut retrieved b5 and b6, submitted 6 and 7 Tanushree Tunstall 2021-02-20 13:05:30 +00:00
• e8644d7af5 dynamut retrieved b5 and b6, submitted 6 and 7 Tanushree Tunstall 2021-02-20 13:05:30 +00:00
• 2995299179 code to retrieve results from batch 4 and 5 once ready Tanushree Tunstall 2021-02-19 12:09:26 +00:00
• d27b5898f7 code to retrieve results from batch 4 and 5 once ready Tanushree Tunstall 2021-02-19 12:09:26 +00:00
• f9249d7bf2 updated .gitignore Tanushree Tunstall 2021-02-18 12:01:04 +00:00
• b12a7769ca updated .gitignore Tanushree Tunstall 2021-02-18 12:01:04 +00:00
• d683e971d4 updated .gitignore to include temp dirs Tanushree Tunstall 2021-02-18 11:54:36 +00:00
• 0c563274b4 updated .gitignore to include temp dirs Tanushree Tunstall 2021-02-18 11:54:36 +00:00
• 8dc3a790c0 add files Tanushree Tunstall 2021-02-18 11:50:46 +00:00
• 8e68fb8f6a add files Tanushree Tunstall 2021-02-18 11:50:46 +00:00
• 69b62e54a5 running dynamut in batches Tanushree Tunstall 2021-02-18 11:27:20 +00:00
• ce5b545703 running dynamut in batches Tanushree Tunstall 2021-02-18 11:27:20 +00:00
• cfdd18086a renamed files in dynamut for consistency Tanushree Tunstall 2021-02-18 10:52:51 +00:00
• ff2bc78645 renamed files in dynamut for consistency Tanushree Tunstall 2021-02-18 10:52:51 +00:00
• 9a0e98eb24 renamed file in mcsm_na to be consistent Tanushree Tunstall 2021-02-18 10:51:17 +00:00
• 84fccfbbb6 renamed file in mcsm_na to be consistent Tanushree Tunstall 2021-02-18 10:51:17 +00:00
• 2168007f12 renaming file Tanushree Tunstall 2021-02-18 10:48:06 +00:00
• 501492f9fb renaming file Tanushree Tunstall 2021-02-18 10:48:06 +00:00
• 19d89230f5 renamed file run_submit to run_submit_dynamut Tanushree Tunstall 2021-02-18 10:45:35 +00:00
• 96e101cf15 renamed file run_submit to run_submit_dynamut Tanushree Tunstall 2021-02-18 10:45:35 +00:00
• a9a4483aee renamed file run_results to run_get_results Tanushree Tunstall 2021-02-18 10:43:45 +00:00
• 06df7369de renamed file run_results to run_get_results Tanushree Tunstall 2021-02-18 10:43:45 +00:00
• cd06a83e13 ran mcsm_na for all 26 batches for gid Tanushree Tunstall 2021-02-16 13:55:31 +00:00
• 4d3389264d ran mcsm_na for all 26 batches for gid Tanushree Tunstall 2021-02-16 13:55:31 +00:00
• 013bba2503 sunmitting mcsm_na jobs manually Tanushree Tunstall 2021-02-16 10:51:06 +00:00
• c02a55c167 sunmitting mcsm_na jobs manually Tanushree Tunstall 2021-02-16 10:51:06 +00:00
• b69d9d729a added get_results_mcsm_na.py run_get_results.py to retrieve results for each batch run of 20 for mcsm_na Tanushree Tunstall 2021-02-15 12:22:52 +00:00
• 3925c4fd29 added get_results_mcsm_na.py run_get_results.py to retrieve results for each batch run of 20 for mcsm_na Tanushree Tunstall 2021-02-15 12:22:52 +00:00
• 7a74fecbda saving work for mcsm_na Tanushree Tunstall 2021-02-15 12:22:19 +00:00
• 4df1c54674 saving work for mcsm_na Tanushree Tunstall 2021-02-15 12:22:19 +00:00
• 322979406c added mcsm_na_temp Tanushree Tunstall 2021-02-12 17:40:02 +00:00
• 0d58c4800b added mcsm_na_temp Tanushree Tunstall 2021-02-12 17:40:02 +00:00
• 1f72001689 added shell script to format muts for mcsm NA Tanushree Tunstall 2021-02-12 17:38:42 +00:00
• 84970a667c added shell script to format muts for mcsm NA Tanushree Tunstall 2021-02-12 17:38:42 +00:00
• c99f1cac92 added mcsm_na scripts to submit batches of 20 Tanushree Tunstall 2021-02-12 16:51:41 +00:00
• a6f1f65acf added mcsm_na scripts to submit batches of 20 Tanushree Tunstall 2021-02-12 16:51:41 +00:00
• b2397ea99d minor cody tidy up Tanushree Tunstall 2021-02-12 16:50:34 +00:00
• 7c84e8b044 minor cody tidy up Tanushree Tunstall 2021-02-12 16:50:34 +00:00
• 9c221e6786 tested and added note to reflect that tar.gz needs to be made into a cmd line option Tanushree Tunstall 2021-02-12 15:32:16 +00:00
• 26fe956d47 tested and added note to reflect that tar.gz needs to be made into a cmd line option Tanushree Tunstall 2021-02-12 15:32:16 +00:00