integration of new mutation density to deepCSA#339
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FerriolCalvet merged 2 commits into272-new-mutation-rate-per-consequence-typefrom Aug 13, 2025
Merged
integration of new mutation density to deepCSA#339FerriolCalvet merged 2 commits into272-new-mutation-rate-per-consequence-typefrom
FerriolCalvet merged 2 commits into272-new-mutation-rate-per-consequence-typefrom
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* Mutability-adjusted mutation density calculation * Fix: module out variable not matching subworkflow * Several small fixes: bug in tuple variable * Permisson error in python script * Fix unnecessary output argument in python script * Fix typo in "depths_df" variable name * Fix sample name variable in python script * Missing sample_name in correction factor function * Adjust output filename in script for consistency * Keep the index (genes) when writing the output * New logfoldchange plots as an output * Fix syntax typo in python script * Fix import * Fix import seaborn * integration of new mutation density to deepCSA (#339) * connect mut_density with pipeline's utils * apply changes from PR #338 * fix bug introduced in reviewing * add samplename to output files * add name to index for storing * keep current directory structure of outputs - mutdensityadj contains new mutation density results -mutdensity keeps having the old computation --------- Co-authored-by: Ferriol Calvet <38539786+FerriolCalvet@users.noreply.github.com> Co-authored-by: FerriolCalvet <ferriolcalvet@gmail.com>
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