Push pc_remove, select_samples, zero_imputation + test#8
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up114 wants to merge 3 commits intoCenikLab:mainfrom
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Push pc_remove, select_samples, zero_imputation + test#8up114 wants to merge 3 commits intoCenikLab:mainfrom
up114 wants to merge 3 commits intoCenikLab:mainfrom
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pc_remove: clean up redundant transpose/reordering stepsselect_samples: require zero-imputed inputs instead of handling zero imputation internallyzero_imputation: update simple imputation to replace zeros with the minimum non-zero value, capped at 1; intersect RIBO and RNA matrices at the end to account for dropped samplestest-zero_imputation: update tests for the new simple-imputation behavior and add a test for the cap-at-1 case