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lightning.git
2023-10-26 Tom Clegg21139: Reduce memory usage in tiling. 21139-import-mem | commitdiff
2023-10-24 Tom CleggFix glm test. | commitdiff
2023-08-29 Alex ColemanMerge branch '20645-updating-dockerfiles' | commitdiff
2023-08-11 Tom CleggMerge branch '20753-fix-missing-columns' | commitdiff
2023-08-02 Tom Clegg20461: Add -pprof-dir option to slice subcommand. | commitdiff
2023-08-02 Alex Coleman20645: Updating base images. 20645-updating-dockerfiles | commitdiff
2023-07-21 Tom Clegg20753: Fix column offset in full matrix when ref tile... 20753-fix-missing-columns | commitdiff
2023-07-20 Alex ColemanUpdating lightning Dockerfile to go from `pip3 install... | commitdiff
2023-07-06 Tom CleggDefault to applying min-coverage filter based on traini... | commitdiff
2023-06-30 Alex ColemanRemove Jiayong as Maintainer, update base images from... | commitdiff
2023-06-27 Tom CleggFix error message. | commitdiff
2023-06-26 Tom CleggFix wrong array index in PCA mode. | commitdiff
2023-06-26 Tom CleggFix missing struct field. | commitdiff
2023-05-05 Tom CleggMerge branch '19995-glm-freq-threshold' | commitdiff
2023-04-06 Tom Clegg19995: Add -max-frequency filter. 19995-glm-freq-threshold | commitdiff
2023-03-29 Tom Clegg19995: Report MAF in onehot-columns.npy. | commitdiff
2023-03-29 Tom Clegg19995: Use allele frequency, apply min freq cutoff... | commitdiff
2023-03-07 Tom CleggMerge branch '19995-glm-freq-threshold' | commitdiff
2023-03-06 Tom Clegg19995: Skip GLM on variants below frequency threshold. | commitdiff
2023-02-02 Tom CleggMerge branch '19997-glm' | commitdiff
2023-02-02 Tom CleggPreserve pca components from input when writing samples... | commitdiff
2023-02-02 Tom CleggFix validation=0 in samples.csv (should be empty for... | commitdiff
2023-02-02 Tom CleggTurn off auto-retry. | commitdiff
2023-01-27 Jiayong LiMerge branch '19868-pca-in-ml' into main | commitdiff
2023-01-27 Jiayong LiMerge branch 'main' into 19868-pca-in-ml 19868-pca-in-ml | commitdiff
2023-01-27 Jiayong LiChange resource requirement of gvcf2fasta and imputation | commitdiff
2023-01-20 Tom CleggDarker colors. | commitdiff
2023-01-20 Tom CleggBring back genomewideline/suggestiveline options. | commitdiff
2023-01-20 Jiayong LiMerge branch '19868-pca-in-ml' into main | commitdiff
2023-01-20 Jiayong LiMerge branch 'main' into 19868-pca-in-ml | commitdiff
2023-01-20 Jiayong LiChange slice-numpy-onehot parameter | commitdiff
2023-01-19 Tom CleggGenerate a manhattan plot for each chromosome. | commitdiff
2023-01-13 Tom CleggFix GLM p-value calculation when -case-control-only... | commitdiff
2023-01-12 Jiayong LiMerge branch '19868-pca-in-ml' into main | commitdiff
2023-01-12 Jiayong LiMerge branch 'main' into 19868-pca-in-ml | commitdiff
2023-01-12 Jiayong LiFix shebang and license | commitdiff
2023-01-10 Tom CleggFix -min-coverage calculation broken when -case-control... | commitdiff
2023-01-03 Tom CleggAdd column headings to slice-numpy -pca sample list... | commitdiff
2023-01-03 Tom CleggFix validation flag in slice-numpy -pca sample list... | commitdiff
2022-12-21 Tom CleggMerge branch '19526-manhattan-plot' | commitdiff
2022-12-19 Tom Clegg19526: Output tile locations and pvalues at specified... 19526-manhattan-plot | commitdiff
2022-12-19 Tom CleggMerge branch '19566-glm' | commitdiff
2022-12-19 Tom Clegg19566: Preemptible flag. | commitdiff
2022-12-19 Tom Clegg19566: Record number of p-value calculations performed. | commitdiff
2022-12-16 Tom Clegg19566: Silence logging from glm library. 19566-glm | commitdiff
2022-12-16 Tom Clegg19566: Fix chi2 used instead of logistic regression... | commitdiff
2022-12-15 Jiayong LiMerge branch '19785-add-cwl' into main | commitdiff
2022-12-15 Jiayong LiMerge branch 'main' into 19785-add-cwl 19785-add-cwl | commitdiff
2022-12-15 Jiayong LiChange lightning docker file so that it builds the... | commitdiff
2022-12-15 Tom Clegg19566: Merge branch 'main' | commitdiff
2022-12-15 Tom CleggMerge branch '19526-manhattan-plot' | commitdiff
2022-12-14 Tom Clegg19566: Precompute cov glm. | commitdiff
2022-12-13 Tom CleggMerge branch '19566-glm' | commitdiff
2022-12-12 Tom Clegg19566: Test p-value vs. Python. | commitdiff
2022-12-12 Tom Clegg19566: Normalize pca values before glm. | commitdiff
2022-12-12 Tom Clegg19566: Add constant, check GLM results against Python. | commitdiff
2022-12-09 Jiayong LiMerge branch '19785-add-cwl' into main | commitdiff
2022-12-09 Jiayong LiFix readme | commitdiff
2022-12-09 Jiayong LiMerge branch '19785-add-cwl' into main | commitdiff
2022-12-09 Jiayong LiAdd cwl and docker files | commitdiff
2022-12-01 Tom Clegg19526: Tidy manhattan plot. | commitdiff
2022-11-29 Tom Clegg19566: Option to limit pca components used in glm.... | commitdiff
2022-11-29 Tom Clegg19566: glm one column at a time. | commitdiff
2022-11-29 Tom Clegg19566: Logistic regression p-value. | commitdiff
2022-11-28 Tom CleggMerge branch '19526-manhattan-plot' | commitdiff
2022-11-28 Tom Clegg19526: Add manhattan plot. | commitdiff
2022-11-18 Tom CleggCheck for unparsed command line args. | commitdiff
2022-11-18 Tom Clegg19780: Fix indexing error. | commitdiff
2022-11-16 Tom Clegg19527: slice-numpy accepts samples.csv with or without... | commitdiff
2022-11-16 Tom Clegg19527: Update arvados sdk. | commitdiff
2022-11-16 Tom Clegg19527: Fix odd # columns to pca. | commitdiff
2022-11-16 Tom Clegg19527: Fix one-hot matrix. | commitdiff
2022-11-16 Tom Clegg19527: Enable choose-samples to work without case/contr... | commitdiff
2022-11-16 Tom Clegg19527: Fix Χ² calculation. | commitdiff
2022-11-16 Tom Clegg19527: Output samples.csv earlier. | commitdiff
2022-11-16 Tom Clegg19527: Fix crash on tag skipped for min-coverage. | commitdiff
2022-11-16 Tom Clegg19527: Option to exclude non-case/control samples. | commitdiff
2022-11-10 Tom CleggMerge branch '19527-training-set' | commitdiff
2022-11-09 Tom Clegg19527: Accommodate header row in samples csv. 19527-training-set | commitdiff
2022-11-09 Tom Clegg19527: Ignore empty line at EOF. | commitdiff
2022-11-09 Tom CleggMerge branch '19524-pca' | commitdiff
2022-11-09 Tom Clegg19527: Fix p-value calculation. | commitdiff
2022-11-09 Tom Clegg19527: Load training-set flag from samples.csv. | commitdiff
2022-11-09 Tom Clegg19527: choose-samples: training/validation set. | commitdiff
2022-11-09 Tom Clegg19527: Load training-set flag from samples.csv. | commitdiff
2022-11-07 Tom Cleggchoose-samples: training/validation set. | commitdiff
2022-11-02 Tom Clegg19524: Fit PCA to specified training set. | commitdiff
2022-10-31 Tom CleggMerge branch '19524-pca' | commitdiff
2022-10-21 Tom Clegg19524: Fix matrix alloc size. 19524-pca | commitdiff
2022-10-20 Tom Clegg19524: Flags choose which PCA components to plot. | commitdiff
2022-10-20 Tom Clegg19524: Update colors, plot unknown-phenotype behind... | commitdiff
2022-10-20 Tom Clegg19524: Limit size of PCA input matrix. | commitdiff
2022-10-19 Tom Clegg19524: Limit size of PCA input matrix. | commitdiff
2022-10-19 Tom Clegg19524: configurable vcpus/ram | commitdiff
2022-10-14 Tom CleggMerge branch '19524-pca' | commitdiff
2022-10-14 Tom Clegg19524: Use marker shape to indicate second category... | commitdiff
2022-10-14 Tom Clegg19524: Remove obsolete pca cmds. | commitdiff
2022-10-14 Tom Clegg19524: Fix deprecated scipy.load. | commitdiff
2022-10-14 Tom Clegg19524: Read multiple phenotype files. | commitdiff
2022-10-14 Tom Clegg19524: Generalize plot colors a little. | commitdiff
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