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2022-01-22generate lineplotAlexander Kabui
2022-01-22minor fix:read input data from json fileAlexander Kabui
2022-01-22export json dataAlexander Kabui
2022-01-22get significant interactionsAlexander Kabui
2022-01-22perform the ctl scanAlexander Kabui
2022-01-22fetch genotypes and phenotype filesAlexander Kabui
2022-01-22init script ctl analysisAlexander Kabui
2021-12-22Refactor wgcna (#63)Alexander Kabui
* add r as a gn3 input * calculate powers from user input * fix merge conflict
2021-11-11Merge branch 'main' into feature/add_rqtl_pairscanzsloan
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 23:43:16 +0000