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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
2024-10-28refactor: 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
2024-09-27Fix Pair-Scan output pathsFrederick Muriuki Muriithi
Related to 4940195460008192b6ca6269e1fb8c172ada4f17c
2024-09-27Fix R/qtl output pathszsloan
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
2024-09-12Make sure dir exists before running R/qtlPjotr Prins
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