Commit graph

Select branches

Hide pull requests

embb_dev

gidb_dev

master

#1

Mono Color

• bc12dbd7c2 added run_7030.py that runs as cmd for all gene targets and sampling methods and outputs a single csv Tanushree Tunstall 2022-06-21 20:37:53 +01:00
• 5b0ccdfec4 added ml_data_fg.py Tanushree Tunstall 2022-06-21 18:21:41 +01:00
• 11ef627150 removed _dissected files and renamed them to _fg Tanushree Tunstall 2022-06-21 18:20:22 +01:00
• fe0986aa28 adde script to run ml baseline models orig version with feature groups Tanushree Tunstall 2022-06-21 18:17:56 +01:00
• 137f19a285 saving work Tanushree Tunstall 2022-06-21 18:12:31 +01:00
• 7b378ca6f3 adding formatting to get all output from ML for feature grpups starting with genomics Tanushree Tunstall 2022-06-21 14:08:12 +01:00
• cadaed2ba7 ML logs Tanushree Tunstall 2022-06-20 21:55:47 +01:00
• 4c5afa614f python scripts for original analysis with logs Tanushree Tunstall 2022-06-20 21:54:48 +01:00
• 8d8fc03f72 added test script to test dissected model Tanushree Tunstall 2022-06-20 21:53:15 +01:00
• e68a153883 working on dissected model, testing diff feature groups Tanushree Tunstall 2022-06-20 21:51:07 +01:00
• 135efcee41 added option to add confusion matrix and target numbers in the mult function Tanushree Tunstall 2022-06-20 17:08:22 +01:00
• 905327bf4e script to run models based on group of features Tanushree Tunstall 2022-06-20 14:59:02 +01:00
• 4ab99dcbd2 saving work for yesterday where uq runs were repeated Tanushree Tunstall 2022-06-20 14:57:11 +01:00
• efeaf52cde added ml runs for complete data with _cd_ in filenames reflecting this Tanushree Tunstall 2022-06-18 19:36:33 +01:00
• 9bc26c1947 slight formatting for existing scripts Tanushree Tunstall 2022-06-18 19:35:49 +01:00
• a53fce5455 added notes for running ml scripts Tanushree Tunstall 2022-06-18 14:45:48 +01:00
• e176d018cb added log files for these ml runs Tanushree Tunstall 2022-06-18 14:44:02 +01:00
• 5bd8ba33f7 added scripts for reverse training Tanushree Tunstall 2022-06-18 14:43:35 +01:00
• d85415daf8 added scripts for scaling law split Tanushree Tunstall 2022-06-18 14:42:46 +01:00
• 4037641dfa added data and ml scripts for 8020 splits Tanushree Tunstall 2022-06-18 14:42:02 +01:00
• 2e50a555a0 minor formatting consistency for 7030 scripts Tanushree Tunstall 2022-06-18 14:41:05 +01:00
• e05e4e2e38 added script for running 7030 split Tanushree Tunstall 2022-06-17 18:28:26 +01:00
• 91e868736c changed dir to allow ml script to import functions Tanushree Tunstall 2022-06-17 18:27:20 +01:00
• e6d3692445 changed dir for reading func in pnca_config.py Tanushree Tunstall 2022-06-17 16:37:07 +01:00
• 96d4e61dca added baseline config files for running v2 ml analysis Tanushree Tunstall 2022-06-17 14:14:26 +01:00
• 05dd9698c4 added aa_index data for running ml Tanushree Tunstall 2022-06-17 13:41:25 +01:00
• 39ccd6cdf4 initial adding of ml scripts for baseline models Tanushree Tunstall 2022-06-17 13:40:09 +01:00
• f355846dae added active site indication for merged_dfs in count_vars_ML.R and also added 'gene_name' in combining_dfs.py Tanushree Tunstall 2022-06-15 18:36:28 +01:00
• 1204f1faba added scripts and files to make AA index work for all drug targets, add header to the aa index output and fetch the aa index headers Tanushree Tunstall 2022-06-15 11:24:07 +01:00
• 03321c261e working new_aa.sh Tanushree Tunstall 2022-06-13 22:05:41 +01:00
• c4ae6d2412 improved aa script Tanushree Tunstall 2022-06-13 21:48:44 +01:00
• 2307a19d86 added example bash cmds Tanushree Tunstall 2022-06-13 21:22:49 +01:00
• 40c4d382f4 added eg to run aaindex from a diff dir Tanushree Tunstall 2022-06-13 21:15:12 +01:00
• bd7d01c7e6 various aa_index_scripts Tanushree Tunstall 2022-06-13 09:42:48 +01:00
• 0c316e4a41 renamed aa_index folder to aa_index_scripts Tanushree Tunstall 2022-05-30 02:24:54 +01:00
• 650d357afc reran to output merged_df3 and merged_df2 csvs from count_vars.ML Tanushree Tunstall 2022-05-29 03:10:51 +01:00
• f41cd0082e moved mmcsm_provean_ed_combine_CHECKS.py to scratch for when I need ED data for merging Tanushree Tunstall 2022-05-25 08:52:40 +01:00
• 1baf7fa9f0 lf Tanushree Tunstall 2022-05-25 23:39:44 +01:00
• 8e65d75b58 added checks before comnining provean and mmcsm_lig Tanushree Tunstall 2022-05-25 08:51:37 +01:00
• a2bcc3a732 added mmcsm_lig and provean dfs merges in comnining_df.py Tanushree Tunstall 2022-05-25 08:50:33 +01:00
• d8041fb494 added count_vars_ML.R to check numbers for revised counts Tanushree Tunstall 2022-05-05 19:32:34 +01:00
• 39566ceadd lineage labels gsub now redundant in combining_dfs_plotting.R Tanushree Tunstall 2022-05-05 19:31:00 +01:00
• d61d11e020 Merge branch 'master' of https://git.tunstall.in/tanu/LSHTM_analysis Tanushree Tunstall 2022-05-05 13:36:03 +01:00
• e54ae877a8 updated data extraction to ensure genes without common mutations and duplicate indices can run from the cmd Tanushree Tunstall 2022-05-05 13:35:24 +01:00
• 4f22cd3db1 various tweaks to make the RShiny dashboards work Tanushree Tunstall 2022-04-28 20:20:41 +01:00
• 5429b8fed7 saving data extraction updated script Tanushree Tunstall 2022-04-28 13:02:30 +01:00
• e419d320ac saving data extraction with final processing Tanushree Tunstall 2022-04-27 12:09:14 +01:00
• 3c436f0c27 finally revised data processing is complete Tanushree Tunstall 2022-04-27 11:09:36 +01:00
• ac0d14e116 done but getting an error when running from cmd Tanushree Tunstall 2022-04-26 17:03:40 +01:00
• 29e9d10e39 add chek for lin index duplicates before output Tanushree Tunstall 2022-04-25 18:38:04 +01:00
• 1371704685 got to the lineage extraction bit Tanushree Tunstall 2022-04-25 18:37:01 +01:00
• 0867827ec6 saved section for generating revised dst Tanushree Tunstall 2022-04-25 16:51:28 +01:00
• cb93cef3c7 did all other mappings until dst column Tanushree Tunstall 2022-04-23 11:14:34 +01:00
• 7a10b4f223 phewwww! finally resolved counts for ambiguous muts Tanushree Tunstall 2022-04-22 17:51:11 +01:00
• 3cd7b36c59 updated data_extraction Tanushree Tunstall 2022-04-22 15:18:08 +01:00
• bf7060baa9 finally added all the lineage calculations Tanushree Tunstall 2022-04-15 14:41:04 +01:00
• 95a73efdd2 saving work with sections reflecting activities Tanushree Tunstall 2022-04-14 19:43:14 +01:00
• e99c169b35 saving work, lineage bits are all over the place, need to rerrange Tanushree Tunstall 2022-04-14 19:39:47 +01:00
• ae3a5500c9 mostly done, now adding lineage magicry Tanushree Tunstall 2022-04-14 19:27:21 +01:00
• f05cb96346 added sections and slotted relevant bits from data_extraction to v2 Tanushree Tunstall 2022-04-14 12:21:16 +01:00
• e6faf80c20 updating ambiguous muts manipulation section in data_extraction_v2 Tanushree Tunstall 2022-04-14 10:36:08 +01:00
• 6330a2e716 added v2 for data extraction Tanushree Tunstall 2022-04-14 10:16:12 +01:00
• 2518556c96 added str.strip() instead of str.lstrip() Tanushree Tunstall 2022-04-08 17:05:24 +01:00
• ac78fe16cd logoP SNP adj Tanushree Tunstall 2022-03-06 14:48:53 +00:00
• 56a6aa8c7e lineage_dist: add all_lineages feature Tanushree Tunstall 2022-03-06 13:31:43 +00:00
• 8fa585417e tweaks for params Tanushree Tunstall 2022-03-02 19:42:24 +00:00
• bf3194259e lineage: toggle for "all lineages" Tanushree Tunstall 2022-03-02 15:54:09 +00:00
• 6c6709e41e various changes Tanushree Tunstall 2022-03-02 11:44:04 +00:00
• 2274f01f23 combined msa and wt seq into 1 list so only list is passed as an arg for plotting ED plots Tanushree Tunstall 2022-02-15 08:31:58 +00:00
• d38521e03a added placeholder defaults for functions in R to make sure that R shiny layput works with a data set for meeting tomorrow Tanushree Tunstall 2022-02-14 19:33:00 +00:00
• 0460ca1708 added consurf plot function and corresponding test script Tanushree Tunstall 2022-02-14 11:16:30 +00:00
• 18e1f14455 saving changes Tanushree Tunstall 2022-02-14 11:14:40 +00:00
• 6ffb084546 added hbond residues in config for all genes Tanushree Tunstall 2022-02-09 15:59:18 +00:00
• 7a14655ecb added active site positions to all config.R Tanushree Tunstall 2022-02-03 18:02:27 +00:00
• 04cddbbf2b minor formatting, taken a line off the barplots_subcolours_aa_PS.R Tanushree Tunstall 2022-02-02 19:01:13 +00:00
• 3e5191f5c6 attempting to visualise consurf plot along with highlighting active site pos Tanushree Tunstall 2022-02-02 19:00:23 +00:00
• 9c3818fd98 added NOTE to the barplots_subcolours_aa_PS.R as I am trying it for other plots Tanushree Tunstall 2022-02-02 18:59:33 +00:00
• d13484e8f5 added function lineage_plot_data.R and corresponding test script, also renamed corr_plot_df.R to corr_plot_data and corresponing test script Tanushree Tunstall 2022-02-01 16:25:58 +00:00
• 3d45780c1a updated docs for dm_om_data.R Tanushree Tunstall 2022-02-01 16:23:03 +00:00
• e795c00831 added gene conditions to test_dm_om_data.R Tanushree Tunstall 2022-02-01 10:54:10 +00:00
• b2e035d9bc moved old dm_om_data_nf to redundant/ Tanushree Tunstall 2022-01-31 17:52:29 +00:00
• ef1fb96b88 tested dm_om_data function with alr gene to make sure valid dfs are being returned Tanushree Tunstall 2022-01-31 17:50:12 +00:00
• 5779b3fe87 added function to get wf and lf data and corresponding test Tanushree Tunstall 2022-01-31 17:36:34 +00:00
• a287b801f7 saving before commiting Tanushree Tunstall 2022-01-31 17:36:00 +00:00
• ea931b59f3 relaced ligand_distance with the variable Tanushree Tunstall 2022-01-30 09:47:56 +00:00
• 8df4a85798 deleted accidental blank line Tanushree Tunstall 2022-01-29 18:10:38 +00:00
• 6b7b5e6c98 saving work Tanushree Tunstall 2022-01-29 18:08:07 +00:00
• cd772e9df1 moved corr_data.R to redundant/ Tanushree Tunstall 2022-01-29 17:34:18 +00:00
• 1035547309 added function to extract data for correlation plots and corresponding test script Tanushree Tunstall 2022-01-29 17:31:02 +00:00
• a4a4890634 added FIXME to fix dm_om data for targets other than gid Tanushree Tunstall 2022-01-29 17:30:19 +00:00
• 5346431256 repurposing corr_data.R into a function to allow required params to be passed in Tanushree Tunstall 2022-01-29 17:24:15 +00:00
• 7317156bba updated docs for the logo functions and tested all of them again Tanushree Tunstall 2022-01-26 15:53:53 +00:00
• 2f7f40efb1 added a few tweaks to check logoplots Tanushree Tunstall 2022-01-26 15:22:13 +00:00
• 1b20f09075 tested edplot with alr gene Tanushree Tunstall 2022-01-26 13:35:57 +00:00
• 8750e3126a renamed logoP.R --> logoP_or.R Tanushree Tunstall 2022-01-26 12:37:08 +00:00
• a2da95ef7c added ed_pfm_data.R function and its corresponding test Tanushree Tunstall 2022-01-26 11:55:38 +00:00
• 5f9a95ccb1 moved Header_TT.R from plotting/ to scripts Tanushree Tunstall 2022-01-26 11:54:38 +00:00
• dec6c72fb5 more header_tt Tanushree Tunstall 2022-01-26 11:50:50 +00:00
• 586927ca56 wholesale change for Header_TT.R location Tanushree Tunstall 2022-01-26 11:39:03 +00:00
• b133b8be24 save content Tanushree Tunstall 2022-01-26 11:34:59 +00:00