genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Expand)	Author
2022-01-22	minor refactoring	Alexander Kabui
2022-01-22	function override:fix target specific output file for network	Alexander Kabui
2022-01-22	generate network	Alexander Kabui
2022-01-22	generate ctl plots for each trait	Alexander Kabui
2022-01-22	fixes for ctl script:generate ctl ctl_significant json	Alexander Kabui
2022-01-22	bugfixes for script;create pheno and geno objects	Alexander Kabui
2022-01-22	generate lineplot	Alexander Kabui
2022-01-22	minor fix:read input data from json file	Alexander Kabui
2022-01-22	export json data	Alexander Kabui
2022-01-22	get significant interactions	Alexander Kabui
2022-01-22	perform the ctl scan	Alexander Kabui
2022-01-22	fetch genotypes and phenotype files	Alexander Kabui
2022-01-22	init script ctl analysis	Alexander Kabui
2021-12-22	Refactor wgcna (#63)...* add r as a gn3 input * calculate powers from user input * fix merge conflict	Alexander Kabui
2021-11-11	Merge branch 'main' into feature/add_rqtl_pairscan	zsloan
2021-10-29	Feature/biweight reimplementation (#47)...* 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	Alexander Kabui
2021-10-25	minor fixes for sript enable annotations	Alexander Kabui
2021-10-25	script modification : add debug statements	Alexander Kabui
2021-10-14	Fixed when model is set to account for situations with no covariates	zsloan
2021-10-14	Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.R	zsloan
2021-10-12	Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/f...	zsloan
2021-10-12	Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into featu...	zsloan
2021-09-27	remove unnecessary comments and variables	Alexander Kabui
2021-09-23	Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ...	zsloan
2021-09-23	Added line priting pair-scan results to CSV and changed the default step-size...	zsloan
2021-09-23	- Added scan_func function that determines whether scanone or scantwo...(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	zsloan
2021-09-23	Added option for running pairscan to rqtl_wrapper.R	zsloan
2021-09-23	Fix covariates as described by Danny	zsloan
2021-09-23	add traits as columns names and pass as json input	Alexander Kabui
2021-09-23	check for na powerEst and use a default value	Alexander Kabui
2021-09-23	append input to output	Alexander Kabui
2021-09-23	sample output data	Alexander Kabui
2021-09-23	validate required output	Alexander Kabui
2021-09-23	add mock test data for script	Alexander Kabui
2021-09-23	pass json file path as an arg	Alexander Kabui
2021-09-23	pass other variables from user input for network constr	Alexander Kabui
2021-09-23	load data from json file and and convert to dt	Alexander Kabui
2021-09-15	minor fixes	Alexander Kabui
2021-09-15	rename variables && delete debugs	Alexander Kabui
2021-09-15	Fetch IMAGE_DIR env and add img location	Alexander Kabui
2021-09-14	remove debug statements	Alexander Kabui
2021-09-14	function to generate rand str for image	Alexander Kabui
2021-09-14	plot plotDendroAndColors and generate png	Alexander Kabui
2021-09-14	construct gene co-expression network & module detection	Alexander Kabui
2021-09-14	compute the softthreshhold	Alexander Kabui
2021-09-14	Checking data for excessive missing values	Alexander Kabui
2021-09-14	load the required data for analysis	Alexander Kabui
2021-09-14	init commit for wgcna script	Alexander Kabui
2021-08-28	Fix issue that caused R/qtl to not use the first covariate when using stratif...	zsloan
2021-08-26	Added # permutations to verbose print	zsloan