Removing design matrix workaround #691
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grst
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Dec 26, 2024
Zethson
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Jan 4, 2025
* Switch to formulaic-contrasts * Cleanup * removing design matrix workaround (#691) Co-authored-by: Emma Dann <emmadann@comino.stanford.edu> * Fix PyDESeq2 * Update tests * fix typo in gitignore * Remove contrast dataclass, which isnt used anywhere * Fix edgeR rpy2 tests (#692) * fix broken rpy2 edger tests * updated edger tests * Fix tests (scipy) Signed-off-by: zethson <lukas.heumos@posteo.net> * submodule Signed-off-by: zethson <lukas.heumos@posteo.net> * Remove unused code Signed-off-by: zethson <lukas.heumos@posteo.net> * type hints Signed-off-by: zethson <lukas.heumos@posteo.net> --------- Signed-off-by: zethson <lukas.heumos@posteo.net> Co-authored-by: Emma Dann <32264060+emdann@users.noreply.github.com> Co-authored-by: Emma Dann <emmadann@comino.stanford.edu> Co-authored-by: zethson <lukas.heumos@posteo.net>
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PR Checklist
docsis updatedDescription of changes
Closes #690
Removed updates to design matrix, no longer needed with PyDESeq2 using formulaic + test
Technical details
Additional context