| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-05-08 | Add extra procedure for parsing a genotype file | BonfaceKilz | |
| * gn3/computations/parsers.py (parse_genofile): New procedure. * tests/unit/computations/test_parsers.py: New test files for above. | |||
| 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 | |
| 2021-05-02 | delete dataset and trait files | 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 | |
| 2021-04-15 | test endpoint for fetching probeset data types | 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 | |
| 2021-04-06 | delete unnecessary functions and comments | Alexander Kabui | |
| 2021-04-05 | fix for fetching dataset traits data | Alexander Kabui | |
| 2021-04-04 | refactor code for trait data | Alexander Kabui | |
| modify unittest and integration tests for datasets | |||
| 2021-04-03 | add tests for getting trait data | Alexander Kabui | |
| 2021-03-31 | add mysqlclient in guix | Alexander Kabui | |
| add env variable for GN2_URL | |||
| 2021-03-31 | add datasets functions and endpoints | Alexander Kabui | |
| 2021-03-30 | refactor retrieve trait sample data and tests | Alexander Kabui | |
| 2021-03-30 | modify getting sample data from db | Alexander Kabui | |
| 2021-03-30 | initial commit for creating dataset | Alexander Kabui | |
| 2021-03-30 | initial commit for creating trait and datasets | 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> | |||
| 2021-03-10 | Fix k-compute command when "loco" is true | BonfaceKilz | |
| 2021-03-08 | Remove unused imports | BonfaceKilz | |
| 2021-03-08 | Delete "generate_gemma_computation_cmd" | BonfaceKilz | |
| 2021-03-08 | Add generic fn for computing k and gwa values | BonfaceKilz | |
| 2021-03-08 | Apply pep-8 formatting | BonfaceKilz | |
| Began using elpy's format code fn | |||
| 2021-03-08 | Move "generate_random_n_string" to file_utils | BonfaceKilz | |
| * gn3/computations/gemma.py (generaten_random_n_string): Move to... * gn3/file_utils.py: ... here. | |||
| 2021-03-08 | Fix failing tests | BonfaceKilz | |
| 2021-02-24 | Create a new helper function for generating k_values and GWA | BonfaceKilz | |
| 2021-02-24 | Add procedure that checks whether a list of paths exist | BonfaceKilz | |
| 2021-02-24 | Check if phenotype exists before creating one | BonfaceKilz | |
| 2021-02-24 | Add new procedure that computes the hash of an array of strings | BonfaceKilz | |
| 2021-02-24 | Add mypy-typing to function | BonfaceKilz | |
| * gn3/computations/gemma.py (generate_random_n_string): Add typing to function. | |||
| 2021-02-24 | Append random 6 chars to generated phenotype file | BonfaceKilz | |
| 2021-02-24 | Create a new method for generating a valid phenotype file on the fly | BonfaceKilz | |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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