| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2025-07-17 | Skip blank lines. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-17 | Skip malformed genotype rows with mismatched data columns. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Add kludge comment for "HSNIH-Palmer_true.geno" which has floats. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Set a larger map size for the larger genotype files. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Add functionality for importing one entire genotype directory. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | More efficiently and correctly count nrows is genotype. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Delete un-used import. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Add module doc-string. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Improve genotype file parsing. | Munyoki Kilyungi | |
| * scripts/lmdb_matrix.py (GenotypeMatrix): Delete transpose. Add "file_info" field. (save_excursion, count_lines): Delete. (get_genotype_dimensions, read_genotype_headers): New function. (read_geno_file): Rename this to... (read_genotype_file): ... this. (genotype_db_put): Put "file_info". (genotype_db_get): Fetch "file_info". (import_genotype): Use read_genotype_file. (print_current_matrix): Remove transpose. Print out file_info metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Simplify genotype db script. | Munyoki Kilyungi | |
| Hashing and versioning made the script very slow. Now, this script can handle much larger data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-07-16 | Add genotype matrix script. | Munyoki Kilyungi | |
| * scripts/lmdb_matrix.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-04-30 | Revert commit dd9ef90ee89e5c075acbd5ef63cb89518e726ca3. | Alexander_Kabui | |
| 2025-04-30 | refactor: For genetic probabilites use cores 0 to use all | Alexander_Kabui | |
| available of no cores detected. | |||
| 2025-04-08 | refactor: Explicity define no of cores for rqtl2 computation. | Alexander_Kabui | |
| 2025-04-08 | refactor: Check for geno_tranposed and founder_geno_transposed. | Alexander_Kabui | |
| 2025-03-27 | refactor: Temporary disable checking sex covariates in rqtl2. | Alexander_Kabui | |
| 2025-03-07 | refactor: Construct map object from cross with columns (Marker, chr,cM, Mb). | Alexander_Kabui | |
| 2025-03-07 | fix: Minor rqtl2 fixes. | Alexander_Kabui | |
| 2025-03-07 | refactor rqtl2 script. | Alexander_Kabui | |
| 2025-03-04 | Revert "feat: Add Python implementation of Fibonacci number calculation". | Munyoki Kilyungi | |
| This reverts commit 280c5e97d21501c03f672ed3576ae3eddfc76420. | |||
| 2025-03-04 | feat: Add Python implementation of Fibonacci number calculation | Munyoki Kilyungi (aider) | |
| 2025-02-28 | Fix linting errors. | Frederick Muriuki Muriithi | |
| 2025-02-24 | Remove "generate_lod_plot" from rqtl2_wrapper.R. | Munyoki Kilyungi | |
| * scripts/rqtl2_wrapper.R (generate_lod_plot): Delete function. (output): Remove "lod_plot_path". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2025-02-21 | feat: Temporary disable performing genome scan with covariates for RQTL2. | Alexander_Kabui | |
| 2025-02-20 | refactor: Skip permutation test when NO_OF_PERMUTATION less than 0. | Alexander_Kabui | |
| 2025-02-20 | refactor: Use p=0.63 in permutation summary for suggestive threshold. | Alexander_Kabui | |
| 2025-02-07 | fix: pass the correct genome probabilites. | Alexander_Kabui | |
| 2025-02-06 | feat: Add the physical map file path. | Alexander_Kabui | |
| 2025-02-06 | refactor: Rename pheno_map to physical_map . | Alexander_Kabui | |
| 2025-02-06 | feat: Pass scan results file and genotype map file as output. | Alexander_Kabui | |
| 2025-02-06 | feat: Modify default thresholds and write permutation results to csv file. | Alexander_Kabui | |
| 2025-01-28 | Pass in virtuoso ttl directory as a CLI option | Frederick Muriuki Muriithi | |
| Pass in the directory as a command-line option to add flexibility to the deployment. Prior to this commit, the script made the assumption that the TTL directory would show up on the path "/var/lib/data", which is not always the case. | |||
| 2025-01-06 | feat: Add print statements for start and end of qtl script run. | Alexander_Kabui | |
| 2024-12-20 | feat: Enable verbose for script by default. | Alexander_Kabui | |
| 2024-11-11 | feat: add step to insert pseudomarkers to the gmap. | Alexander_Kabui | |
| 2024-11-11 | fix: fix issue fetching covar: | Alexander_Kabui | |
| 2024-11-11 | refactor: rename dataset to cross. | Alexander_Kabui | |
| 2024-11-11 | feat: add a threshold argument for lod score peak with default 1. | Alexander_Kabui | |
| 2024-11-11 | feat: print_help when certain parameters are not provided. | Alexander_Kabui | |
| 2024-11-11 | Refactor: remove requirement for input and output file to be in the | Alexander_Kabui | |
| same directory. | |||
| 2024-11-11 | Refactor: add better message for computation steps. | Alexander_Kabui | |
| 2024-11-11 | refactor: refactor output for preprocessing steps. | Alexander_Kabui | |
| 2024-11-11 | Refactor: refactor checks for working directory, input and output file. | Alexander_Kabui | |
| 2024-11-11 | refactor: remove stringr as a script dependency: | Alexander_Kabui | |
| refactor: refactor use of str_glue to cat. | |||
| 2024-11-11 | refactor: refactor for using cat and new line. | Alexander_Kabui | |
| 2024-11-11 | refactor: use NO_OF_CORES as default and pass control file to arguments. | Alexander_Kabui | |
| 2024-11-11 | refactor: adding pseudomarkers o genetic probabilites map. | Alexander_Kabui | |
| 2024-11-11 | refactor: refactor printing out lod thresholds. | Alexander_Kabui | |
| 2024-11-11 | export qtl effect plots for multi parent populations. | Alexander_Kabui | |
| 2024-11-11 | feat: add plots for qtl effect multi parent population. | Alexander_Kabui | |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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