| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-11-11 | feat: implementation for multiparent genome scan. | Alexander_Kabui | |
| 2024-11-11 | feat: export chromosome names and qtl effects. | Alexander_Kabui | |
| 2024-11-08 | feat: init add functionality to estimate qtl effect. | Alexander_Kabui | |
| 2024-10-30 | feat: add option for using pstrata for permutation. | Alexander_Kabui | |
| 2024-10-30 | Refactor: Remove reduntant code. | Alexander_Kabui | |
| Fix issue when computing the kinship | |||
| 2024-10-29 | Refactor: pre compute kinship for both permutation and genome scan. | Alexander_Kabui | |
| 2024-10-29 | Refactor: remove hardcoded dir_path for control files. | Alexander_Kabui | |
| 2024-10-29 | Refactor: make plot in the temp directory passed in the script arguments. | Alexander_Kabui | |
| 2024-10-29 | feat: add output_file as a command line argument. | Alexander_Kabui | |
| 2024-10-29 | Refactor: ensure the temp directory is not null. | Alexander_Kabui | |
| ensure the input_file exists in the working directory. | |||
| 2024-10-29 | feat: add optparse for the arguments. | Alexander_Kabui | |
| 2024-10-29 | feat: write output results as json. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactor code to find lod peaks. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactoring for code to perform permutation tests. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactor function to generate plots from scan1 function. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactor method to compute scan 1. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactor function to calculate error LOD scores. | Alexander_Kabui | |
| 2024-10-29 | Refactor: refactor functions to compute genetic probabilities: | Alexander_Kabui | |
| 2024-10-29 | Refactor: cleanup comments. | Alexander_Kabui | |
| 2024-10-29 | Refactor: use FALSE for better defaults. | Alexander_Kabui | |
| 2024-10-29 | feat: add defaults for creating cross objects. | Alexander_Kabui | |
| 2024-10-28 | refactor: Minor fixes for file, remove comments | Alexander_Kabui | |
| 2024-10-25 | feat: add function to fetch load peaks for 1 QTL. | Alexander_Kabui | |
| 2024-10-25 | Minor fix. | Alexander_Kabui | |
| 2024-10-25 | Refactor: apply code formatting. | Alexander_Kabui | |
| 2024-10-25 | feat: add code to perform permutation for single Qtl. | Alexander_Kabui | |
| 2024-10-25 | feat: add method to generate LOD curves for the genome scan. | Alexander_Kabui | |
| 2024-10-25 | feat: Add method to perform 1 pair scan. | Alexander_Kabui | |
| 2024-10-25 | feat: add code to perform genetic probabilities. | Alexander_Kabui | |
| 2024-10-24 | feat: create implementation for creating cross object using r-qtl2. | Alexander_Kabui | |
| 2024-09-27 | Fix Pair-Scan output paths | Frederick Muriuki Muriithi | |
| Related to 4940195460008192b6ca6269e1fb8c172ada4f17c | |||
| 2024-09-27 | Fix R/qtl output paths | zsloan | |
| The script now takes the --outdir parameter as the output directory, only using TMPDIR if nothing is passed "output" in the output directory was also changed to "gn3" to be consistent with recent changes to GN3's code | |||
| 2024-09-12 | Make sure dir exists before running R/qtl | Pjotr Prins | |
| 2024-09-12 | Getting Rqtl to run on fallback | Pjotr Prins | |
| 2024-07-23 | chore: add logging info | John Nduli | |
| 2024-07-23 | chore: mypy and pylint fixes | John Nduli | |
| 2024-07-23 | fix: resolve duplicate errors when updating data | John Nduli | |
| 2024-07-23 | refactor: clean query for insert | John Nduli | |
| 2024-07-23 | refactor: clean up insert query | John Nduli | |
| 2024-07-23 | refactor: reorganize update_rif script to be more pythonic | John Nduli | |
| 2024-07-23 | chore: fix pylint errors | John Nduli | |
| 2024-07-23 | refactor: rename addRIf to update_rif_table.py | John Nduli | |
| 2024-07-12 | Rename hash_rdf_graph -> md5hash_ttl_dir. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-07-12 | Use correct ttl-dir path when generating checksums. | Munyoki Kilyungi | |
| * scripts/index-genenetwork (is_data_modified): Provide directory instead of specific ttl file. (create_xapian_index): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-07-12 | fix: remove .py extension for addRif to prevent pylint checks | John Nduli | |
| 2024-07-12 | refactor: fix mypy and pylint errors | John Nduli | |
| 2024-07-12 | feat: copy addRif script from genenetwork1 | John Nduli | |
| original: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/maintainance/addRif.py Included some changes to make it python3 compatible | |||
| 2024-07-08 | Pass output directory to R/qtl script instead of pulling it from the | zsloan | |
| environment Also fixes issue where the control marker keyword was wrong | |||
| 2024-07-03 | Return a "-1" if the turtle directory does not exist. | Munyoki Kilyungi | |
| * scripts/index-genenetwork (hash_rdf_graph): Remove check for the turtle directory. (is_data_modified): Ditto. (create_xapian_index): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-07-03 | Generate a checksum for all the ttl files. | Munyoki Kilyungi | |
| * scripts/index-genenetwork (hash_generif_graph): Rename to hash_rdf_graph. Generate a checksum of all the turtle files inside the ttl directory that's the basis for the GN virtuoso graph. (create_xapian_index): Rename hash_generif_graph -> hash_rdf_graph. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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