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• e4270b67c8 saving work for today Tanushree Tunstall 2020-07-14 16:13:17 +01:00
• f8fef60475 saving work for today Tanushree Tunstall 2020-07-14 16:13:17 +01:00
• 2bc5be20b9 resolving merge conflicts dur to shoddy data Tanushree Tunstall 2020-07-14 14:09:42 +01:00
• f27c223bdd resolving merge conflicts dur to shoddy data Tanushree Tunstall 2020-07-14 14:09:42 +01:00
• 7d36e0e36b fixed white space prob with mcsm input with merge Tanushree Tunstall 2020-07-14 14:07:23 +01:00
• 8dc2fa7326 fixed white space prob with mcsm input with merge Tanushree Tunstall 2020-07-14 14:07:23 +01:00
• 46b1505fdf remove white space in colnames before mcsm format output Tanushree Tunstall 2020-07-14 12:59:40 +01:00
• 5a2084ba11 remove white space in colnames before mcsm format output Tanushree Tunstall 2020-07-14 12:59:40 +01:00
• 83383b4493 finding discrepancy in merging or dfs,grrrr Tanushree Tunstall 2020-07-13 18:31:29 +01:00
• c0827b56cc finding discrepancy in merging or dfs,grrrr Tanushree Tunstall 2020-07-13 18:31:29 +01:00
• 9e8469abe3 trying to resolve copy warning in code Tanushree Tunstall 2020-07-13 12:20:43 +01:00
• da0c03c2e0 trying to resolve copy warning in code Tanushree Tunstall 2020-07-13 12:20:43 +01:00
• 57a966c7c4 added sanity checks for or_kinship calcs Tanushree Tunstall 2020-07-13 11:37:43 +01:00
• 5655af42c0 added sanity checks for or_kinship calcs Tanushree Tunstall 2020-07-13 11:37:43 +01:00
• f9500d5324 added sanity checks for or_kin Tanushree Tunstall 2020-07-10 15:24:57 +01:00
• 167b051ae7 added sanity checks for or_kin Tanushree Tunstall 2020-07-10 15:24:57 +01:00
• 5677175423 refactoring or_kin script minor changes only Tanushree Tunstall 2020-07-10 12:38:42 +01:00
• cb31c5c8f4 refactoring or_kin script minor changes only Tanushree Tunstall 2020-07-10 12:38:42 +01:00
• c80faef0bf refactoring or_kin script minor changes only Tanushree Tunstall 2020-07-10 12:37:41 +01:00
• 6cedc3c14d refactoring or_kin script minor changes only Tanushree Tunstall 2020-07-10 12:37:41 +01:00
• aaf3f5e084 added cleaned up af_or_calcs.R Tanushree Tunstall 2020-07-09 15:55:16 +01:00
• 4fd3462fc8 added cleaned up af_or_calcs.R Tanushree Tunstall 2020-07-09 15:55:16 +01:00
• d3d82623d2 added consistent style scripts to format kd & rd values Tanushree Tunstall 2020-07-09 14:08:27 +01:00
• 7b50dc3a3a added consistent style scripts to format kd & rd values Tanushree Tunstall 2020-07-09 14:08:27 +01:00
• e4a7deae7b minor tidy up in foldx, mcsm and dssp scripts Tanushree Tunstall 2020-07-09 14:04:16 +01:00
• 08379c0def minor tidy up in foldx, mcsm and dssp scripts Tanushree Tunstall 2020-07-09 14:04:16 +01:00
• 0379d3e241 renamed mcsm_wrapper to run_mcsm Tanushree Tunstall 2020-07-09 13:33:56 +01:00
• 44597ec563 renamed mcsm_wrapper to run_mcsm Tanushree Tunstall 2020-07-09 13:33:56 +01:00
• 91348aaae2 added dssp.py with refactored argeparse Tanushree Tunstall 2020-07-09 12:58:55 +01:00
• c0fa9e3904 added dssp.py with refactored argeparse Tanushree Tunstall 2020-07-09 12:58:55 +01:00
• f8e345f5bc adding default dirs and filenames to argparse in foldx and mcsm Tanushree Tunstall 2020-07-09 12:57:08 +01:00
• 6725f08829 adding default dirs and filenames to argparse in foldx and mcsm Tanushree Tunstall 2020-07-09 12:57:08 +01:00
• 6402990154 minor edits to format mcsm data like sorting df Tanushree Tunstall 2020-07-09 11:15:56 +01:00
• 6961a9cdb3 minor edits to format mcsm data like sorting df Tanushree Tunstall 2020-07-09 11:15:56 +01:00
• 01fbc2a87b ran foldx and mcsm (get) for 33k dataset Tanushree Tunstall 2020-07-08 20:30:32 +01:00
• 8931441fa5 ran foldx and mcsm (get) for 33k dataset Tanushree Tunstall 2020-07-08 20:30:32 +01:00
• 0e71b23759 modified extraction to be explicit for extracting nsSNP for specified gene Tanushree Tunstall 2020-07-08 18:47:22 +01:00
• 172fa18420 modified extraction to be explicit for extracting nsSNP for specified gene Tanushree Tunstall 2020-07-08 18:47:22 +01:00
• 1fa0dc6ad4 minor changes in data extraction Tanushree Tunstall 2020-07-08 16:01:54 +01:00
• 436125745d minor changes in data extraction Tanushree Tunstall 2020-07-08 16:01:54 +01:00
• c958cc1081 data extraction tidy up Tanushree Tunstall 2020-07-08 13:26:33 +01:00
• 65e6b28d9e data extraction tidy up Tanushree Tunstall 2020-07-08 13:26:33 +01:00
• a4670b9944 saving work for the day Tanushree Tunstall 2020-07-07 18:31:14 +01:00
• e4328df255 saving work for the day Tanushree Tunstall 2020-07-07 18:31:14 +01:00
• a7f21cfb14 adding clean files for rerrun 35k dataset Tanushree Tunstall 2020-07-07 18:28:55 +01:00
• 8f460347b4 adding clean files for rerrun 35k dataset Tanushree Tunstall 2020-07-07 18:28:55 +01:00
• 943513a338 added script to combine all files in one Tanushree Tunstall 2020-07-07 16:06:11 +01:00
• 0973717287 added script to combine all files in one Tanushree Tunstall 2020-07-07 16:06:11 +01:00
• 5addb85851 renamed files that combine dfs Tanushree Tunstall 2020-07-07 15:46:13 +01:00
• 01ef04613a renamed files that combine dfs Tanushree Tunstall 2020-07-07 15:46:13 +01:00
• a220288c5f testing combining df script Tanushree Tunstall 2020-07-03 19:23:23 +01:00
• 56d1617561 testing combining df script Tanushree Tunstall 2020-07-03 19:23:23 +01:00
• 262bd79204 stil fiddling iwth combining dfs Tanushree Tunstall 2020-07-03 19:22:46 +01:00
• b09c15004b stil fiddling iwth combining dfs Tanushree Tunstall 2020-07-03 19:22:46 +01:00
• 90cbb49560 added fixme: for some necessary required changes Tanushree Tunstall 2020-07-02 14:16:40 +01:00
• e0ba3108f6 added fixme: for some necessary required changes Tanushree Tunstall 2020-07-02 14:16:40 +01:00
• f758c01159 added combining funct & combining_mcsm_foldx script Tanushree Tunstall 2020-07-01 16:41:58 +01:00
• fb277a1484 added combining funct & combining_mcsm_foldx script Tanushree Tunstall 2020-07-01 16:41:58 +01:00
• 4d686e2933 refactor foldx pipeline to include: * command-line args * creating necessary dirs automagically * code cleanup, syntax errors, etc etc Tanushree Tunstall 2020-06-30 17:14:30 +01:00
• 973a1a33da refactor foldx pipeline to include: * command-line args * creating necessary dirs automagically * code cleanup, syntax errors, etc etc Tanushree Tunstall 2020-06-30 17:14:30 +01:00
• af65a86ff9 updated code and made it tidy Tanushree Tunstall 2020-06-25 14:40:44 +01:00
• e8a66a7a94 updated code and made it tidy Tanushree Tunstall 2020-06-25 14:40:44 +01:00
• 3c6122a296 tidying script Tanushree Tunstall 2020-06-25 13:12:09 +01:00
• 7032baa08d tidying script Tanushree Tunstall 2020-06-25 13:12:09 +01:00
• b82cc11dbe updated ref dict to create separate dicts Tanushree Tunstall 2020-06-24 14:10:39 +01:00
• cdb1ea1476 updated ref dict to create separate dicts Tanushree Tunstall 2020-06-24 14:10:39 +01:00
• 626ed3a57b added commonly used mutation format for missense muts in the gene_specific nssnp_info file Tanushree Tunstall 2020-06-24 13:34:35 +01:00
• 27a656dba1 added commonly used mutation format for missense muts in the gene_specific nssnp_info file Tanushree Tunstall 2020-06-24 13:34:35 +01:00
• a298071309 combined and output all ors Tanushree Tunstall 2020-06-23 17:34:54 +01:00
• a9498f8e08 combined and output all ors Tanushree Tunstall 2020-06-23 17:34:54 +01:00
• 003b22ce3f script for calcuating various OR & output csv Tanushree Tunstall 2020-06-23 13:07:29 +01:00
• d8b272b0ae script for calcuating various OR & output csv Tanushree Tunstall 2020-06-23 13:07:29 +01:00
• a1cc7ee33d further tidy for OR calcs Tanushree Tunstall 2020-06-23 12:19:26 +01:00
• c80c87235e further tidy for OR calcs Tanushree Tunstall 2020-06-23 12:19:26 +01:00
• 1e43ca8136 tody scracth script for various OR calcs Tanushree Tunstall 2020-06-23 11:57:51 +01:00
• e3ae1c3a95 tody scracth script for various OR calcs Tanushree Tunstall 2020-06-23 11:57:51 +01:00
• 18998092f4 all OR calcs using sapply and output as df Tanushree Tunstall 2020-06-22 18:17:06 +01:00
• 263527f576 all OR calcs using sapply and output as df Tanushree Tunstall 2020-06-22 18:17:06 +01:00
• 8f272bdc17 extracting other params from logistic Tanushree Tunstall 2020-06-22 14:11:16 +01:00
• 6b5ced65e5 extracting other params from logistic Tanushree Tunstall 2020-06-22 14:11:16 +01:00
• ada205962b script to combine ors and afs Tanushree Tunstall 2020-06-22 13:07:26 +01:00
• 28e52d4194 script to combine ors and afs Tanushree Tunstall 2020-06-22 13:07:26 +01:00
• 0c3c6fd143 script to combine all ors Tanushree Tunstall 2020-06-19 14:43:23 +01:00
• c98ca7c8ae script to combine all ors Tanushree Tunstall 2020-06-19 14:43:23 +01:00
• 3497d1ef54 renamed files & added or kinship link file Tanushree Tunstall 2020-06-19 10:33:26 +01:00
• 07258120de renamed files & added or kinship link file Tanushree Tunstall 2020-06-19 10:33:26 +01:00
• fa2bcb5f05 updated Af and OR calcs script with argeparse and minor tidyup Tanushree Tunstall 2020-06-18 18:37:55 +01:00
• c36197d75e updated Af and OR calcs script with argeparse and minor tidyup Tanushree Tunstall 2020-06-18 18:37:55 +01:00
• 76ecb65a1a getopt and commandArgs examples, and AF/OR update to use getopt() Tanushree Tunstall 2020-06-18 17:59:28 +01:00
• f9a8ed3dc7 getopt and commandArgs examples, and AF/OR update to use getopt() Tanushree Tunstall 2020-06-18 17:59:28 +01:00
• 6c2c7e0a90 removed merging df for AF_OR Tanushree Tunstall 2020-06-18 16:10:02 +01:00
• 864f814e1b removed merging df for AF_OR Tanushree Tunstall 2020-06-18 16:10:02 +01:00
• b33419c939 af and or calcs, not merging Tanushree Tunstall 2020-06-18 15:57:25 +01:00
• 3d1536f2b6 af and or calcs, not merging Tanushree Tunstall 2020-06-18 15:57:25 +01:00
• 010ef133dd foramtting and adding or Tanushree Tunstall 2020-06-18 13:55:45 +01:00
• c4f9e24007 foramtting and adding or Tanushree Tunstall 2020-06-18 13:55:45 +01:00
• fdba990b80 added AF_and OR calcs script and making it generic Tanushree Tunstall 2020-06-17 19:36:34 +01:00
• b73c506587 added AF_and OR calcs script and making it generic Tanushree Tunstall 2020-06-17 19:36:34 +01:00
• 8d1daabff4 ran struc param analysis Tanushree Tunstall 2020-06-17 19:36:02 +01:00
• 2cebd338ba ran struc param analysis Tanushree Tunstall 2020-06-17 19:36:02 +01:00