LSHTM_analysis

tanu/LSHTM_analysis

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d6a63eed21 added mut_landscape.R that outputs the mutational positions and annotations for generating the structural landscape of all gene-targets Tanushree Tunstall 2022-07-30 19:22:07 +01:00
26f284d76e added test_func_combined.py Tanushree Tunstall 2022-07-29 00:14:39 +01:00
9cd6613da6 added cm_logo_skf_v2.py Tanushree Tunstall 2022-07-29 00:13:54 +01:00
e55906d2c7 saving work Tanushree Tunstall 2022-07-29 00:12:43 +01:00
1695e90b42 running none_complete with diff cv threhsolds Tanushree Tunstall 2022-07-28 15:33:43 +01:00
85f59155fa uncommented all models for a full run Tanushree Tunstall 2022-07-28 15:28:31 +01:00
37f5199c5c added the cm_ml_iterator_TODO.py for later Tanushree Tunstall 2022-07-28 15:25:31 +01:00
e32308d984 moved old logs Tanushree Tunstall 2022-07-28 15:24:49 +01:00
fd0ccc9032 added genes_ml_logs Tanushree Tunstall 2022-07-28 15:23:49 +01:00
cd68e60f09 updated running_scripts with added rt and none and none_bts Tanushree Tunstall 2022-07-28 15:22:44 +01:00
d3d5698a3e added MultClfs_CVs.py and ml_iterator_CVs.py Tanushree Tunstall 2022-07-28 15:19:58 +01:00
b87f8d0295 trying diff cv thresholds for single gene Tanushree Tunstall 2022-07-28 15:19:13 +01:00
8d8a61675f various edits Tanushree Tunstall 2022-07-28 13:19:30 +01:00
90b9477520 ml_iterator tweaks Tanushree Tunstall 2022-07-28 13:19:46 +01:00
584b866f0b moved ../ml_functions/MultClfs_logo_skf.py to del Tanushree Tunstall 2022-07-28 12:25:29 +01:00
2c50124b1b moved logo_skf function to del as using the MultClfs for combined data Tanushree Tunstall 2022-07-28 12:24:24 +01:00
a6532ddfa3 just running for pnca Tanushree Tunstall 2022-07-27 17:11:30 +01:00
744bc8f4a1 added dummy classifier to models Tanushree Tunstall 2022-07-27 17:10:04 +01:00
c32005c99c adding other split types on ml_iterator Tanushree Tunstall 2022-07-27 15:58:15 +01:00
63c8876764 checking the splitTTS script to make sure other splits have been factored in Tanushree Tunstall 2022-07-27 15:52:20 +01:00
f4cab1fdfb fixed masking condition for ML training data for genes and wrote revised mask files out Tanushree Tunstall 2022-07-27 13:36:16 +01:00
0adf69f75a added model names sklearn Tanushree Tunstall 2022-07-16 15:35:42 +01:00
39e72b2dfb added all_estimators Tanushree Tunstall 2022-07-16 13:32:19 +01:00
a590354f15 saving work from panino Tanushree Tunstall 2022-07-12 10:12:41 +01:00
33e3b5a0a6 various bugs Tanushree Tunstall 2022-07-10 20:00:35 +01:00
6950c4b057 added reverse traininig as split type in SplitTTS.py Tanushree Tunstall 2022-07-11 20:03:06 +01:00
1965517681 added other split_type options i.e none and none with bts Tanushree Tunstall 2022-07-11 19:27:14 +01:00
ce730fbe57 uncommented Tanushree Tunstall 2022-07-10 13:29:01 +01:00
350be30f19 minor changes to run combined_model Tanushree Tunstall 2022-07-10 13:23:13 +01:00
057c98c2f1 updated rs Tanushree Tunstall 2022-07-10 13:04:51 +01:00
e37442efd2 updated ml_iterator function args Tanushree Tunstall 2022-07-10 13:03:14 +01:00
9594d0a328 uncommented models for logo Tanushree Tunstall 2022-07-10 12:53:51 +01:00
4d5b848471 iterator Tanushree Tunstall 2022-07-10 12:33:17 +01:00
01ff9d5be6 added instructions to run individual genes Tanushree Tunstall 2022-07-10 12:45:45 +01:00
3b4cfecc9f added target_count_numbers.py Tanushree Tunstall 2022-07-10 12:43:00 +01:00
de5c1270be added Mult_clfs_logo and Mult_clsf.py with consistency Tanushree Tunstall 2022-07-10 12:32:52 +01:00
06f2ce97b6 minor var name fix for MultClfs.py and ml_iterator Tanushree Tunstall 2022-07-09 11:02:37 +01:00
ef52fd7a94 saving before running Tanushree Tunstall 2022-07-09 10:59:26 +01:00
e07fa3bc05 rerunning ml_iteraror.py Tanushree Tunstall 2022-07-09 10:58:14 +01:00
8bde6f0640 minor var bame update in ml_iterator Tanushree Tunstall 2022-07-09 10:52:50 +01:00
8079dd7b6c reran to generate merged_df3 with correct dst for dst muts. modified combining_dfs_plotting.R Tanushree Tunstall 2022-07-08 21:33:57 +01:00
289c8913d0 added MultClds_SIMPLE.py to simplify my function to run without blind test Tanushree Tunstall 2022-07-08 13:54:49 +01:00
880ef46099 added CHECK_model Tanushree Tunstall 2022-07-08 13:53:44 +01:00
23799275a0 saving work from thinkpad Tanushree Tunstall 2022-07-08 13:53:17 +01:00
5577f5b195 fucking shit count vars Tanushree Tunstall 2022-07-07 20:26:36 +01:00
3e18193a36 added examples Tanushree Tunstall 2022-07-07 17:46:06 +01:00
f57f25f47a various changes to count_vars_ML.R Tanushree Tunstall 2022-07-07 12:31:57 +01:00
d14c3f9c4a adde dummy classifier Tanushree Tunstall 2022-07-07 12:28:58 +01:00
a15d801c2a tried pca Tanushree Tunstall 2022-07-05 23:05:37 +01:00
8d831f3613 added different scaling options Tanushree Tunstall 2022-07-05 22:47:13 +01:00
ebef0c7967 added test script to see one gene Tanushree Tunstall 2022-07-05 16:06:24 +01:00
79cb89a019 saving work Tanushree Tunstall 2022-07-05 16:06:03 +01:00
652cf4802e added MultClfs_fi to add FI scores for models, in development Tanushree Tunstall 2022-07-05 14:19:35 +01:00
53c229f480 added random state to split in function Tanushree Tunstall 2022-07-05 14:15:43 +01:00
e5f882841e added cm_datai.py to get data for cm model for running fs later Tanushree Tunstall 2022-07-02 16:57:41 +01:00
b2d0b827ad added cm run for logo_skf for actual data Tanushree Tunstall 2022-07-02 16:57:11 +01:00
9071a87056 fs: cut down the number of iterations Tanushree Tunstall 2022-07-02 11:12:39 +01:00
7ba838b493 redo unconfusion Tanushree Tunstall 2022-07-02 10:32:19 +01:00
a166a37c0e undo wrong rename Tanushree Tunstall 2022-07-02 10:31:55 +01:00
5a81511163 filename Tanushree Tunstall 2022-07-02 10:28:10 +01:00
dccd3c8eb2 multiple changes Tanushree Tunstall 2022-07-02 10:25:42 +01:00
2fda32901b change more hardcoded CPU counts to os.cpu_count() Tanushree Tunstall 2022-07-02 10:25:13 +01:00
b8653c6afe ML scripts: {'n_jobs': os.cpu_count() } Tanushree Tunstall 2022-07-02 10:20:40 +01:00
11af00f1db changed ml output dirs and ready to run fs Tanushree Tunstall 2022-07-01 21:40:14 +01:00
57348f1874 added log frile for cm run for complete data with skf Tanushree Tunstall 2022-07-01 20:38:34 +01:00
b7e1b51a31 added ml_iterator_fs.py Tanushree Tunstall 2022-07-01 20:38:08 +01:00
b5777a17c9 saving work Tanushree Tunstall 2022-07-01 20:37:41 +01:00
d812835713 added cm_logo_skf.py and placeholder for splits Tanushree Tunstall 2022-07-01 13:55:12 +01:00
952cfeb4c0 added MultClf for combined model to make changes with cv Tanushree Tunstall 2022-07-01 11:40:23 +01:00
0494765c9b fixed indentation Tanushree Tunstall 2022-07-01 11:38:59 +01:00
7eef463915 TEMP -> ml_iterator Tanushree Tunstall 2022-06-29 22:20:23 +01:00
50cb36f2b3 add iterating iterator of iterators (TEMP) Tanushree Tunstall 2022-06-29 22:12:04 +01:00
cbfa9ff31b lineage plots: be a function and then run over all pairs Tanushree Tunstall 2022-06-29 19:24:47 +01:00
8965bee5d6 LINEAGE2 plots: p value stars Tanushree Tunstall 2022-06-29 17:18:55 +01:00
087170a798 added .py Tanushree Tunstall 2022-06-29 12:08:35 +01:00
9aadb0329f added ml_functions dir Tanushree Tunstall 2022-06-29 12:06:47 +01:00
c85c965c3e added TODO for lineage2.R Tanushree Tunstall 2022-06-29 10:26:08 +01:00
aff7247e3b really!?!?!?!? Tanushree Tunstall 2022-06-28 21:52:04 +01:00
478df927cc horrible lineage analysis hell Tanushree Tunstall 2022-06-28 21:51:02 +01:00
ce0f12382e added a comment to data extraction Tanushree Tunstall 2022-06-28 13:45:59 +01:00
6c10776ea9 saving work Tanushree Tunstall 2022-06-25 14:15:21 +01:00
f99b5d1888 added GetMLData.py for combined model and added to functions including previous ones that have been moved there Tanushree Tunstall 2022-06-25 14:12:07 +01:00
5d38cde912 added all run scripts for diffferent splits Tanushree Tunstall 2022-06-24 20:39:50 +01:00
e2bc384155 added FS to MultClfs.py and modified data for different splits for consistency Tanushree Tunstall 2022-06-24 20:35:53 +01:00
edb7aebd6a saving Tanushree Tunstall 2022-06-24 15:43:00 +01:00
1160ad7268 added running_scripts to keep track Tanushree Tunstall 2022-06-24 15:41:27 +01:00
b37a950fec optimised run_7030.py to generate ouput from dict now that the processfunction and parameter dicts have been added Tanushree Tunstall 2022-06-24 15:40:18 +01:00
7dc7e25016 appened sys.path to allow local imports Tanushree Tunstall 2022-06-24 13:41:07 +01:00
a15ab80bc6 added log_FS_pnca_7030.txt after running FS for pnca Tanushree Tunstall 2022-06-24 13:27:16 +01:00
96f4e7085a added test_MultClfs.py to test the functions now in a single script Tanushree Tunstall 2022-06-24 13:26:42 +01:00
a3c644d04b removed MultModelsCl.py and ProcessMultModelsCl.py as these are merged into a single script for convenience Tanushree Tunstall 2022-06-24 13:25:51 +01:00
fba1481c08 added MultClfs.py that contains my ML functions Tanushree Tunstall 2022-06-24 13:25:00 +01:00
19da36842b removed the two functions MultModelsCl.py and ProcessMultModelsCl.py as these have now been combined Tanushree Tunstall 2022-06-24 13:24:04 +01:00
ad99efedd7 saving work Tanushree Tunstall 2022-06-24 13:21:21 +01:00
3514e1b4ba added run_7030_LOOP.py to loop through the resampling data and get processed output Tanushree Tunstall 2022-06-23 21:29:54 +01:00
1d3190899d added ProcessMultModelsCl.py that processes the output for multiple models Tanushree Tunstall 2022-06-23 21:27:13 +01:00
4fe62c072b added metadata output for running multiple models Tanushree Tunstall 2022-06-23 21:25:00 +01:00
5dea35f97c aaded scripts for FS including test call, etc Tanushree Tunstall 2022-06-23 14:53:01 +01:00
8fe0048328 saving work Tanushree Tunstall 2022-06-23 14:52:27 +01:00
0350784d52 changed blind_test_input_df to blind_test_df in MultModelsCl Tanushree Tunstall 2022-06-22 16:42:04 +01:00