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2024-11-12Pure aesthetics: No functional change.Frederick Muriuki Muriithi
This commit has no functional change it implements. It is purely a aesthetics change to please Frederick.
2024-11-11Allow extra database connection options on URIFrederick Muriuki Muriithi
Update the database URI parsing to allow setting of extra connection option on the URI string.
2024-11-11feat: add step to insert pseudomarkers to the gmap.Alexander_Kabui
2024-11-11fix: fix issue fetching covar:Alexander_Kabui
2024-11-11refactor: rename dataset to cross.Alexander_Kabui
2024-11-11feat: add a threshold argument for lod score peak with default 1.Alexander_Kabui
2024-11-11feat: print_help when certain parameters are not provided.Alexander_Kabui
2024-11-11Refactor: remove requirement for input and output file to be in theAlexander_Kabui
same directory.
2024-11-11Refactor: add better message for computation steps.Alexander_Kabui
2024-11-11refactor: refactor output for preprocessing steps.Alexander_Kabui
2024-11-11Refactor: refactor checks for working directory, input and output file.Alexander_Kabui
2024-11-11refactor: remove stringr as a script dependency:Alexander_Kabui
refactor: refactor use of str_glue to cat.
2024-11-11refactor: refactor for using cat and new line.Alexander_Kabui
2024-11-11refactor: use NO_OF_CORES as default and pass control file to arguments.Alexander_Kabui
2024-11-11refactor: adding pseudomarkers o genetic probabilites map.Alexander_Kabui
2024-11-11refactor: refactor printing out lod thresholds.Alexander_Kabui
2024-11-11export qtl effect plots for multi parent populations.Alexander_Kabui
2024-11-11feat: add plots for qtl effect multi parent population.Alexander_Kabui
2024-11-11feat: implementation for getting meffects for multiparent population.Alexander_Kabui
2024-11-11feat: implementation for multiparent genome scan.Alexander_Kabui
2024-11-11feat: export chromosome names and qtl effects.Alexander_Kabui
2024-11-08feat: init add functionality to estimate qtl effect.Alexander_Kabui
2024-10-30feat: add option for using pstrata for permutation.Alexander_Kabui
2024-10-30Refactor: Remove reduntant code.Alexander_Kabui
Fix issue when computing the kinship
2024-10-29Refactor: pre compute kinship for both permutation and genome scan.Alexander_Kabui
2024-10-29Refactor: remove hardcoded dir_path for control files.Alexander_Kabui
2024-10-29Refactor: make plot in the temp directory passed in the script arguments.Alexander_Kabui
2024-10-29feat: add output_file as a command line argument.Alexander_Kabui
2024-10-29Refactor: ensure the temp directory is not null.Alexander_Kabui
ensure the input_file exists in the working directory.
2024-10-29feat: add optparse for the arguments.Alexander_Kabui
2024-10-29feat: write output results as json.Alexander_Kabui
2024-10-29Refactor: refactor code to find lod peaks.Alexander_Kabui
2024-10-29Refactor: refactoring for code to perform permutation tests.Alexander_Kabui
2024-10-29Refactor: refactor function to generate plots from scan1 function.Alexander_Kabui
2024-10-29Refactor: refactor method to compute scan 1.Alexander_Kabui
2024-10-29Refactor: refactor function to calculate error LOD scores.Alexander_Kabui
2024-10-29Refactor: refactor functions to compute genetic probabilities:Alexander_Kabui
2024-10-29Refactor: cleanup comments.Alexander_Kabui
2024-10-29Refactor: use FALSE for better defaults.Alexander_Kabui
2024-10-29feat: add defaults for creating cross objects.Alexander_Kabui
2024-10-28fix: remove dangerous default configs and have a detailed error with how to ↵John Nduli
configure
2024-10-28refactor: Minor fixes for file, remove commentsAlexander_Kabui
2024-10-25feat: add function to fetch load peaks for 1 QTL.Alexander_Kabui
2024-10-25Minor fix.Alexander_Kabui
2024-10-25Refactor: apply code formatting.Alexander_Kabui
2024-10-25feat: add code to perform permutation for single Qtl.Alexander_Kabui
2024-10-25feat: add method to generate LOD curves for the genome scan.Alexander_Kabui
2024-10-25feat: Add method to perform 1 pair scan.Alexander_Kabui
2024-10-25feat: add code to perform genetic probabilities.Alexander_Kabui
2024-10-24feat: create implementation for creating cross object using r-qtl2.Alexander_Kabui
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-12-02 18:04:59 +0000