| Age | Commit message (Expand) | Author |
|---|---|---|
| 2022-03-22 | Added option for running pairscan to rqtl_wrapper.R | zsloan |
| 2022-03-08 | Create database connections within context managers...Use the `with` context manager to open database connections, so as to ensure that those connections are closed once the call is completed. This hopefully avoids the 'too many connections' error | Frederick Muriuki Muriithi |
| 2022-03-03 | Run partial correlations in an external process...Run the partial correlations code in an external python process decoupling it from the server and making it asynchronous. Summary of changes: * gn3/api/correlation.py: - Remove response processing code - Queue partial corrs processing - Create new endpoint to get results * gn3/commands.py - Compose the pcorrs command to be run in an external process - Enable running of subprocess commands with list args * gn3/responses/__init__.py: new module indicator file * gn3/responses/pcorrs_responses.py: Hold response processing code extracted from ~gn3.api.correlations.py~ file * scripts/partial_correlations.py: CLI script to process the pcorrs * sheepdog/worker.py: - Add the *genenetwork3* path at the beginning of the ~sys.path~ list to override any GN3 in the site-packages - Add any environment variables to be set for the command to be run | Frederick Muriuki Muriithi |
| 2022-02-11 | Quote shell variables to prevent globbing...Quote the shell variables to prevent globbing and word splitting. Deactivate this check for the specific lines that require intentional word splitting | Frederick Muriuki Muriithi |
| 2022-02-02 | Fix R/qtl covar bug...The rqtl_wrapper script was throwing an error when only a single categorical covariate was used. This is apparently because "covars[,name]" throws an error in such a situation. Using just "covars" in such a situation prevents the error. So I just added an if statement checking the number of covariates. There might be some better way to deal with this in R, but this is the best I could come up with. | zsloan |
| 2022-02-02 | remove comments | Alexander Kabui |
| 2022-02-02 | match case string input to boolean | Alexander Kabui |
| 2022-02-02 | fix for parametric input | Alexander Kabui |
| 2022-02-02 | use user input significance | Alexander Kabui |
| 2022-02-02 | new line fix | Alexander Kabui |
| 2022-02-02 | add new json output | Alexander Kabui |
| 2022-01-22 | minor refactoring | Alexander Kabui |
| 2022-01-22 | function override:fix target specific output file for network | Alexander Kabui |
| 2022-01-22 | generate network | Alexander Kabui |
| 2022-01-22 | generate ctl plots for each trait | Alexander Kabui |
| 2022-01-22 | fixes for ctl script:generate ctl ctl_significant json | Alexander Kabui |
| 2022-01-22 | bugfixes for script;create pheno and geno objects | Alexander Kabui |
| 2022-01-22 | generate lineplot | Alexander Kabui |
| 2022-01-22 | minor fix:read input data from json file | Alexander Kabui |
| 2022-01-22 | export json data | Alexander Kabui |
| 2022-01-22 | get significant interactions | Alexander Kabui |
| 2022-01-22 | perform the ctl scan | Alexander Kabui |
| 2022-01-22 | fetch genotypes and phenotype files | Alexander Kabui |
| 2022-01-22 | init script ctl analysis | Alexander Kabui |
| 2021-12-22 | Refactor wgcna (#63)...* add r as a gn3 input * calculate powers from user input * fix merge conflict | Alexander Kabui |
| 2021-10-29 | Feature/biweight reimplementation (#47)...* 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 | Alexander Kabui |
| 2021-10-25 | minor fixes for sript enable annotations | Alexander Kabui |
| 2021-10-25 | script modification : add debug statements | Alexander Kabui |
| 2021-10-14 | Fixed when model is set to account for situations with no covariates | zsloan |
| 2021-10-14 | Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.R | zsloan |
| 2021-10-12 | Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/f... | zsloan |
| 2021-09-27 | remove unnecessary comments and variables | Alexander Kabui |
| 2021-09-23 | Fix covariates as described by Danny | zsloan |
| 2021-09-23 | add traits as columns names and pass as json input | Alexander Kabui |
| 2021-09-23 | check for na powerEst and use a default value | Alexander Kabui |
| 2021-09-23 | append input to output | Alexander Kabui |
| 2021-09-23 | sample output data | Alexander Kabui |
| 2021-09-23 | validate required output | Alexander Kabui |
| 2021-09-23 | add mock test data for script | Alexander Kabui |
| 2021-09-23 | pass json file path as an arg | Alexander Kabui |
| 2021-09-23 | pass other variables from user input for network constr | Alexander Kabui |
| 2021-09-23 | load data from json file and and convert to dt | Alexander Kabui |
| 2021-09-15 | minor fixes | Alexander Kabui |
| 2021-09-15 | rename variables && delete debugs | Alexander Kabui |
| 2021-09-15 | Fetch IMAGE_DIR env and add img location | Alexander Kabui |
| 2021-09-14 | remove debug statements | Alexander Kabui |
| 2021-09-14 | function to generate rand str for image | Alexander Kabui |
| 2021-09-14 | plot plotDendroAndColors and generate png | Alexander Kabui |
| 2021-09-14 | construct gene co-expression network & module detection | Alexander Kabui |
| 2021-09-14 | compute the softthreshhold | Alexander Kabui |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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