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2021-10-29Feature/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
2021-10-25minor fixes for sript enable annotationsAlexander Kabui
2021-10-25script modification : add debug statementsAlexander Kabui
2021-10-14Fixed when model is set to account for situations with no covariateszsloan
2021-10-14Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.Rzsloan
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
bug/fix_rqtl_covariates
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
feature/add_rqtl_pairscan
2021-09-27remove unnecessary comments and variablesAlexander Kabui
2021-09-23Updated 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)
2021-09-23Added 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 scantwozsloan
(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
2021-09-23Added option for running pairscan to rqtl_wrapper.Rzsloan
2021-09-23Fix covariates as described by Dannyzsloan
2021-09-23add traits as columns names and pass as json inputAlexander Kabui
2021-09-23check for na powerEst and use a default valueAlexander Kabui
2021-09-23append input to outputAlexander Kabui
2021-09-23sample output dataAlexander Kabui
2021-09-23validate required outputAlexander Kabui
2021-09-23add mock test data for scriptAlexander Kabui
2021-09-23pass json file path as an argAlexander Kabui
2021-09-23pass other variables from user input for network constrAlexander Kabui
2021-09-23load data from json file and and convert to dtAlexander Kabui
2021-09-15minor fixesAlexander Kabui
2021-09-15rename variables && delete debugsAlexander Kabui
2021-09-15Fetch IMAGE_DIR env and add img locationAlexander Kabui
2021-09-14remove debug statementsAlexander Kabui
2021-09-14function to generate rand str for imageAlexander Kabui
2021-09-14plot plotDendroAndColors and generate pngAlexander Kabui
2021-09-14construct gene co-expression network & module detectionAlexander Kabui
2021-09-14compute the softthreshholdAlexander Kabui
2021-09-14Checking data for excessive missing valuesAlexander Kabui
2021-09-14load the required data for analysisAlexander Kabui
2021-09-14init commit for wgcna scriptAlexander Kabui
2021-08-28Fix issue that caused R/qtl to not use the first covariate when using ↵zsloan
stratified permutations + covariates
2021-08-26Added # permutations to verbose printzsloan
2021-06-23minor fixes for biweight scriptAlexander Kabui
2021-06-22scripts: laminar: Add json with hooks for running a linterBonfaceKilz
2021-06-22scripts: laminar: Add sh scripts for CIBonfaceKilz
2021-06-20merge mainAlexander Kabui
2021-06-20make requested changes to biweightAlexander Kabui
2021-06-18Added option for enabling permutation stratazsloan
Fixed issue where covariates with numerical names were being ignored Fixed issue where the hash filename wasn't being used for the permutation output
2021-06-18Add rqtl_wrapper.R script and necessary imports to guix.scmzsloan
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-29 10:07:13 +0000