| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-05-24 | New script to compute partial correlations | Frederick Muriuki Muriithi | |
| * Add a new script to compute the partial correlations against: - a select list of traits, or - an entire dataset depending on the specified subcommand. This new script is meant to supercede the `scripts/partial_correlations.py` script. * Fix the check for errors * Reorganise the order of arguments for the `partial_correlations_with_target_traits` function: move the `method` argument before the `target_trait_names` argument so that the common arguments in the partial correlation computation functions share the same order. | |||
| 2022-05-05 | Extract common error checking. Rename function. | Frederick Muriuki Muriithi | |
| * Extract the common error checking code into a separate function * Rename the function to make its use clearer | |||
| 2022-03-22 | Merge branch 'feature/add_rqtl_pairscan' of ↵ | zsloan | |
| https://github.com/zsloan/genenetwork3 into feature/add_rqtl_pairscan | |||
| 2022-03-22 | Change order of if statements for running genoprob command | zsloan | |
| Now it checks for pairscan first, just in case interval ends up being passed (which is an irrelevant parameter for pairscan) Also added a couple more verbose prints | |||
| 2022-03-22 | Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ↵ | zsloan | |
| we need the list of markers/pseudomarkers and their positions) | |||
| 2022-03-22 | Added line priting pair-scan results to CSV and changed the default ↵ | zsloan | |
| step-size to 10cM for pair-scan | |||
| 2022-03-22 | - Added scan_func function that determines whether scanone or scantwo | zsloan | |
| (pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints | |||
| 2022-03-22 | Added option for running pairscan to rqtl_wrapper.R | zsloan | |
| 2022-03-08 | Create database connections within context managers | Frederick Muriuki Muriithi | |
| 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 | |||
| 2022-03-03 | Run partial correlations in an external process | Frederick Muriuki Muriithi | |
| 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 | |||
| 2022-02-11 | Quote shell variables to prevent globbing | Frederick Muriuki Muriithi | |
| Quote the shell variables to prevent globbing and word splitting. Deactivate this check for the specific lines that require intentional word splitting | |||
| 2022-02-02 | Fix R/qtl covar bug | zsloan | |
| 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. | |||
| 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) | Alexander Kabui | |
| * add r as a gn3 input * calculate powers from user input * fix merge conflict | |||
| 2021-11-11 | Merge branch 'main' into feature/add_rqtl_pairscan | zsloan | |
| 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 | |||
| 2021-10-25 | 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 ↵ | zsloan | |
| bug/fix_rqtl_covariates | |||
| 2021-10-12 | Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵ | zsloan | |
| feature/add_rqtl_pairscan | |||
| 2021-09-27 | remove unnecessary comments and variables | Alexander Kabui | |
| 2021-09-23 | Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ↵ | zsloan | |
| we need the list of markers/pseudomarkers and their positions) | |||
| 2021-09-23 | Added line priting pair-scan results to CSV and changed the default ↵ | zsloan | |
| step-size to 10cM for pair-scan | |||
| 2021-09-23 | - Added scan_func function that determines whether scanone or scantwo | zsloan | |
| (pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints | |||
| 2021-09-23 | Added option for running pairscan to rqtl_wrapper.R | zsloan | |
| 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 | |
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
| aboutsummaryrefslogtreecommitdiff |