| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-11-11 | pylint fixes and pep8 formatting | Alexander Kabui | |
| 2021-11-11 | fix target and base sample data order | Alexander Kabui | |
| 2021-11-11 | fix:spawned processes memory issues | Alexander Kabui | |
| 2021-11-11 | replace list with generators | Alexander Kabui | |
| 2021-10-29 | Feature/biweight reimplementation (#47) | Alexander Kabui | |
| * add biweight reimplementation with pingouin * delete biweight scripts and tests * add python-pingouin to guix file * delete biweight paths * mypy fix:pingouin mising imports * pep8 formatting && pylint fixes | |||
| 2021-08-20 | Minor correlation fixes (#36) | Alexander Kabui | |
| * fix key error for (*tissue_cor) tissue correlation * update tests for tissue correlation * rename speed_compute to fast_compute * pep8 formatting | |||
| 2021-08-18 | Fix obvious linting errors | Muriithi Frederick Muriuki | |
| * Fix linting errors that do not change the function of the code. | |||
| 2021-08-11 | use normal function for correlation (#34) | Alexander Kabui | |
| * use normal function for correlation + rename functions * update test for sample correlation * use normal function for tissue correlation + rename functions | |||
| 2021-07-26 | Check if corr_coefficient is NaN, since apparently it's stored as NaN ↵ | zsloan | |
| instead of None when it can't be calculcated (which was messing up sorting); it may also be okay to remove the None check, but leaving it for now (#28) | |||
| 2021-06-20 | merge main | Alexander Kabui | |
| 2021-06-20 | make requested changes to biweight | Alexander Kabui | |
| 2021-06-16 | Fixed spelling of coeffient to coefficient | zsloan | |
| 2021-06-14 | add biweight r script and tests | Alexander Kabui | |
| 2021-05-30 | fix index error (#16) | Alexander Kabui | |
| 2021-05-15 | resolve merge conflict | Alexander Kabui | |
| 2021-05-15 | Merge branch 'main' into feature/minor-fixes | Alexander Kabui | |
| 2021-05-15 | index lit tuple result | Alexander Kabui | |
| 2021-05-13 | computations: correlations: Apply pep-8 | BonfaceKilz | |
| 2021-05-12 | delete unused functions | Alexander Kabui | |
| 2021-05-12 | rename lit_correlation_for_trait_list to lit_correlation_for_trait | Alexander Kabui | |
| 2021-05-12 | rename tissue_correlation_for_trait_list with tissue_correlation_for_trait | Alexander Kabui | |
| 2021-05-12 | rename p_val ro tissue_p_value for tissue_results | Alexander Kabui | |
| 2021-05-03 | add default no of cores | Alexander Kabui | |
| 2021-05-03 | add trait_id fix mypy issues | Alexander Kabui | |
| 2021-05-03 | minor fixes for tiss correlation tests and naming | Alexander Kabui | |
| 2021-05-03 | replace database with conn | Alexander Kabui | |
| 2021-04-20 | pep8 formatting | Alexander Kabui | |
| 2021-04-20 | add experiment function for computing tissue correlation using multiprocessing | Alexander Kabui | |
| 2021-04-18 | refactor:return trait_name in corr_results | Alexander Kabui | |
| 2021-04-17 | ad pep8 formatting | Alexander Kabui | |
| 2021-04-17 | add sort for correlation results | Alexander Kabui | |
| refactor return data type for tissue and lit | |||
| 2021-04-16 | add benchmark function for sample r | Alexander Kabui | |
| 2021-04-16 | benchmark normal function for sample r | Alexander Kabui | |
| 2021-04-15 | optimization for sample correlation | Alexander Kabui | |
| 2021-04-12 | fix merge conflict | Alexander Kabui | |
| 2021-04-12 | Integrate correlation API | Alexander Kabui | |
| - add new api for gn2-gn3 sample r integration - delete map for sample list to values - add db util file - add python msql-client dependency - add db for fetching lit correlation results - add unittests for db utils - add tests for db_utils - modify api for fetching lit correlation results - refactor Mock Database Connector and unittests - add sql url parser - add SQL URI env variable - refactor code for db utils - modify return data for lit correlation - refactor tissue correlation endpoint - replace db_instance with conn | |||
| 2021-04-06 | fix Docstrings | Alexander Kabui | |
| 2021-03-23 | Re-add mypy conf file | BonfaceKilz | |
| Deleted in 56ce88a | |||
| 2021-03-17 | gn3: computations: correlations: Apply autopep-8. | BonfaceKilz | |
| 2021-03-16 | Refactor/clean up correlations (#4) | Alexander Kabui | |
| * initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com> | |||
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