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lightning.git
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 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
2022-07-15 Tom CleggAdd test for variant at right end of spanning tile. commit | commitdiff | tree | snapshot
2022-07-15 Tom CleggGenerate annotations for spanning tiles. commit | commitdiff | tree | snapshot
2022-07-14 Tom CleggUpdate tests. commit | commitdiff | tree | snapshot
2022-07-07 Tom CleggFix wrong index in chunk>0 case. commit | commitdiff | tree | snapshot
2022-07-01 Tom CleggFix low-coverage tiles counting toward min coverage... commit | commitdiff | tree | snapshot
2022-06-03 Tom CleggFix loss of precision in p-value calculation. commit | commitdiff | tree | snapshot
2022-05-04 Tom Clegg19073: Fix dup tag detection. commit | commitdiff | tree | snapshot
2022-05-04 Tom Clegg19073: Fix dup tag detection. commit | commitdiff | tree | snapshot
2022-05-03 Tom Clegg19073: Remove dup tags (>1 ref placement) from tilestat... commit | commitdiff | tree | snapshot
2022-04-29 Tom CleggAdd -log10(pvalue) row to onehot-columns.npy output... commit | commitdiff | tree | snapshot
2022-03-16 Tom CleggAdd tilestats cmd. commit | commitdiff | tree | snapshot
2022-03-16 Tom CleggWrite chunk-tag-offset.csv with chunked tilevariant... commit | commitdiff | tree | snapshot
2022-03-04 Tom CleggChange zygosity column info from het=1 to hom=1. commit | commitdiff | tree | snapshot
2022-02-24 Tom CleggFix left-most diff cases. commit | commitdiff | tree | snapshot
2022-02-22 Tom CleggEncode spanning tile as 0 in tile variant matrix. commit | commitdiff | tree | snapshot
2022-02-20 Tom CleggMore debugging info for -debug-tag. commit | commitdiff | tree | snapshot
2022-02-20 Tom CleggSkip input files that aren't needed because -max-tag. commit | commitdiff | tree | snapshot
2022-02-18 Tom CleggFix left-most diff cases. commit | commitdiff | tree | snapshot
2022-02-18 Tom CleggAdd -debug-tag flag. commit | commitdiff | tree | snapshot
2022-02-18 Tom CleggFix -include-variant-1 commit | commitdiff | tree | snapshot
2022-02-17 Tom CleggUpdate tests (don't include both het+hom if only one... commit | commitdiff | tree | snapshot
2022-02-17 Tom CleggFix -max-tag filter. commit | commitdiff | tree | snapshot
2022-02-17 Tom CleggFix sparse one-hot coordinates for chunk n>0. commit | commitdiff | tree | snapshot
2022-02-17 Tom CleggFix -max-tag filter. commit | commitdiff | tree | snapshot
2022-02-15 Tom CleggOption to include variant 1 in one-hot matrix. commit | commitdiff | tree | snapshot
2022-02-11 Tom CleggInclude tiles in one-hot matrix even if there is no... commit | commitdiff | tree | snapshot
2022-02-09 Tom CleggSupport -max-tag flag for debugging. commit | commitdiff | tree | snapshot
2022-02-04 Tom CleggDon't include het just because corresponding hom passed. commit | commitdiff | tree | snapshot
2022-02-04 Tom CleggUpdate logged stats. commit | commitdiff | tree | snapshot
2022-02-04 Tom CleggDon't use tags that appear more than once per sequence. commit | commitdiff | tree | snapshot
2022-02-03 Tom CleggFix log message. commit | commitdiff | tree | snapshot
2022-02-03 Tom CleggSkip tags that appear twice in the same chromosome. commit | commitdiff | tree | snapshot
2022-01-31 Tom CleggAdd dump command. commit | commitdiff | tree | snapshot
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