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lightning.git
2023-04-06 Tom Clegg19995: Add -max-frequency filter. 19995-glm-freq-threshold commit | commitdiff | tree | snapshot
2023-03-29 Tom Clegg19995: Report MAF in onehot-columns.npy. commit | commitdiff | tree | snapshot
2023-03-29 Tom Clegg19995: Use allele frequency, apply min freq cutoff... commit | commitdiff | tree | snapshot
2023-03-07 Tom CleggMerge branch '19995-glm-freq-threshold' commit | commitdiff | tree | snapshot
2023-03-06 Tom Clegg19995: Skip GLM on variants below frequency threshold. commit | commitdiff | tree | snapshot
2023-02-02 Tom CleggMerge branch '19997-glm' commit | commitdiff | tree | snapshot
2023-02-02 Tom CleggPreserve pca components from input when writing samples... commit | commitdiff | tree | snapshot
2023-02-02 Tom CleggFix validation=0 in samples.csv (should be empty for... commit | commitdiff | tree | snapshot
2023-02-02 Tom CleggTurn off auto-retry. commit | commitdiff | tree | snapshot
2023-01-27 Jiayong LiMerge branch '19868-pca-in-ml' into main commit | commitdiff | tree | snapshot
2023-01-27 Jiayong LiMerge branch 'main' into 19868-pca-in-ml 19868-pca-in-ml commit | commitdiff | tree | snapshot
2023-01-27 Jiayong LiChange resource requirement of gvcf2fasta and imputation commit | commitdiff | tree | snapshot
2023-01-20 Tom CleggDarker colors. commit | commitdiff | tree | snapshot
2023-01-20 Tom CleggBring back genomewideline/suggestiveline options. commit | commitdiff | tree | snapshot
2023-01-20 Jiayong LiMerge branch '19868-pca-in-ml' into main commit | commitdiff | tree | snapshot
2023-01-20 Jiayong LiMerge branch 'main' into 19868-pca-in-ml commit | commitdiff | tree | snapshot
2023-01-20 Jiayong LiChange slice-numpy-onehot parameter commit | commitdiff | tree | snapshot
2023-01-19 Tom CleggGenerate a manhattan plot for each chromosome. commit | commitdiff | tree | snapshot
2023-01-13 Tom CleggFix GLM p-value calculation when -case-control-only... commit | commitdiff | tree | snapshot
2023-01-12 Jiayong LiMerge branch '19868-pca-in-ml' into main commit | commitdiff | tree | snapshot
2023-01-12 Jiayong LiMerge branch 'main' into 19868-pca-in-ml commit | commitdiff | tree | snapshot
2023-01-12 Jiayong LiFix shebang and license commit | commitdiff | tree | snapshot
2023-01-10 Tom CleggFix -min-coverage calculation broken when -case-control... commit | commitdiff | tree | snapshot
2023-01-03 Tom CleggAdd column headings to slice-numpy -pca sample list... commit | commitdiff | tree | snapshot
2023-01-03 Tom CleggFix validation flag in slice-numpy -pca sample list... commit | commitdiff | tree | snapshot
2022-12-21 Tom CleggMerge branch '19526-manhattan-plot' commit | commitdiff | tree | snapshot
2022-12-19 Tom Clegg19526: Output tile locations and pvalues at specified... 19526-manhattan-plot commit | commitdiff | tree | snapshot
2022-12-19 Tom CleggMerge branch '19566-glm' commit | commitdiff | tree | snapshot
2022-12-19 Tom Clegg19566: Preemptible flag. commit | commitdiff | tree | snapshot
2022-12-19 Tom Clegg19566: Record number of p-value calculations performed. commit | commitdiff | tree | snapshot
2022-12-16 Tom Clegg19566: Silence logging from glm library. 19566-glm commit | commitdiff | tree | snapshot
2022-12-16 Tom Clegg19566: Fix chi2 used instead of logistic regression... commit | commitdiff | tree | snapshot
2022-12-15 Jiayong LiMerge branch '19785-add-cwl' into main commit | commitdiff | tree | snapshot
2022-12-15 Jiayong LiMerge branch 'main' into 19785-add-cwl 19785-add-cwl commit | commitdiff | tree | snapshot
2022-12-15 Jiayong LiChange lightning docker file so that it builds the... commit | commitdiff | tree | snapshot
2022-12-15 Tom Clegg19566: Merge branch 'main' commit | commitdiff | tree | snapshot
2022-12-15 Tom CleggMerge branch '19526-manhattan-plot' commit | commitdiff | tree | snapshot
2022-12-14 Tom Clegg19566: Precompute cov glm. commit | commitdiff | tree | snapshot
2022-12-13 Tom CleggMerge branch '19566-glm' commit | commitdiff | tree | snapshot
2022-12-12 Tom Clegg19566: Test p-value vs. Python. commit | commitdiff | tree | snapshot
2022-12-12 Tom Clegg19566: Normalize pca values before glm. commit | commitdiff | tree | snapshot
2022-12-12 Tom Clegg19566: Add constant, check GLM results against Python. commit | commitdiff | tree | snapshot
2022-12-09 Jiayong LiMerge branch '19785-add-cwl' into main commit | commitdiff | tree | snapshot
2022-12-09 Jiayong LiFix readme commit | commitdiff | tree | snapshot
2022-12-09 Jiayong LiMerge branch '19785-add-cwl' into main commit | commitdiff | tree | snapshot
2022-12-09 Jiayong LiAdd cwl and docker files commit | commitdiff | tree | snapshot
2022-12-01 Tom Clegg19526: Tidy manhattan plot. commit | commitdiff | tree | snapshot
2022-11-29 Tom Clegg19566: Option to limit pca components used in glm.... commit | commitdiff | tree | snapshot
2022-11-29 Tom Clegg19566: glm one column at a time. commit | commitdiff | tree | snapshot
2022-11-29 Tom Clegg19566: Logistic regression p-value. commit | commitdiff | tree | snapshot
2022-11-28 Tom CleggMerge branch '19526-manhattan-plot' commit | commitdiff | tree | snapshot
2022-11-28 Tom Clegg19526: Add manhattan plot. commit | commitdiff | tree | snapshot
2022-11-18 Tom CleggCheck for unparsed command line args. commit | commitdiff | tree | snapshot
2022-11-18 Tom Clegg19780: Fix indexing error. commit | commitdiff | tree | snapshot
2022-11-16 Tom Clegg19527: slice-numpy accepts samples.csv with or without... commit | commitdiff | tree | snapshot
2022-11-16 Tom Clegg19527: Update arvados sdk. commit | commitdiff | tree | snapshot
2022-11-16 Tom Clegg19527: Fix odd # columns to pca. commit | commitdiff | tree | snapshot
2022-11-16 Tom Clegg19527: Fix one-hot matrix. commit | commitdiff | tree | snapshot
2022-11-16 Tom Clegg19527: Enable choose-samples to work without case/contr... commit | commitdiff | tree | snapshot
2022-11-16 Tom Clegg19527: Fix Χ² calculation. commit | commitdiff | tree | snapshot
2022-11-16 Tom Clegg19527: Output samples.csv earlier. commit | commitdiff | tree | snapshot
2022-11-16 Tom Clegg19527: Fix crash on tag skipped for min-coverage. commit | commitdiff | tree | snapshot
2022-11-16 Tom Clegg19527: Option to exclude non-case/control samples. commit | commitdiff | tree | snapshot
2022-11-10 Tom CleggMerge branch '19527-training-set' commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: Accommodate header row in samples csv. 19527-training-set commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: Ignore empty line at EOF. commit | commitdiff | tree | snapshot
2022-11-09 Tom CleggMerge branch '19524-pca' commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: Fix p-value calculation. commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: Load training-set flag from samples.csv. commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: choose-samples: training/validation set. commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: Load training-set flag from samples.csv. commit | commitdiff | tree | snapshot
2022-11-07 Tom Cleggchoose-samples: training/validation set. commit | commitdiff | tree | snapshot
2022-11-02 Tom Clegg19524: Fit PCA to specified training set. commit | commitdiff | tree | snapshot
2022-10-31 Tom CleggMerge branch '19524-pca' commit | commitdiff | tree | snapshot
2022-10-21 Tom Clegg19524: Fix matrix alloc size. 19524-pca commit | commitdiff | tree | snapshot
2022-10-20 Tom Clegg19524: Flags choose which PCA components to plot. commit | commitdiff | tree | snapshot
2022-10-20 Tom Clegg19524: Update colors, plot unknown-phenotype behind... commit | commitdiff | tree | snapshot
2022-10-20 Tom Clegg19524: Limit size of PCA input matrix. commit | commitdiff | tree | snapshot
2022-10-19 Tom Clegg19524: Limit size of PCA input matrix. commit | commitdiff | tree | snapshot
2022-10-19 Tom Clegg19524: configurable vcpus/ram commit | commitdiff | tree | snapshot
2022-10-14 Tom CleggMerge branch '19524-pca' commit | commitdiff | tree | snapshot
2022-10-14 Tom Clegg19524: Use marker shape to indicate second category... commit | commitdiff | tree | snapshot
2022-10-14 Tom Clegg19524: Remove obsolete pca cmds. commit | commitdiff | tree | snapshot
2022-10-14 Tom Clegg19524: Fix deprecated scipy.load. commit | commitdiff | tree | snapshot
2022-10-14 Tom Clegg19524: Read multiple phenotype files. commit | commitdiff | tree | snapshot
2022-10-14 Tom Clegg19524: Generalize plot colors a little. commit | commitdiff | tree | snapshot
2022-10-13 Tom CleggFail if inadvertently using randomness. commit | commitdiff | tree | snapshot
2022-10-12 Tom Clegg19524: Fix colormap. commit | commitdiff | tree | snapshot
2022-10-12 Tom Clegg19524: propagate pca-components arg. commit | commitdiff | tree | snapshot
2022-10-11 Tom Clegg19524: plot: get sample list from csv instead of fasta... commit | commitdiff | tree | snapshot
2022-10-11 Tom Clegg19524: Output PCA. commit | commitdiff | tree | snapshot
2022-10-07 Tom CleggUpdate deps, improve error reporting commit | commitdiff | tree | snapshot
2022-10-07 Tom CleggUse min-coverage filter commit | commitdiff | tree | snapshot
2022-08-05 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-08-03 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-07-27 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-07-27 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-07-27 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-07-26 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-07-20 Tom CleggFix crash when ref tile is dropped due to duplicate... commit | commitdiff | tree | snapshot
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