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Custom dispersion de#288

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stemangiola merged 45 commits intomasterstemangiola/tidybulk:masterfrom custom-dispersion-DEstemangiola/tidybulk:custom-dispersion-DECopy head branch name to clipboardAug 29, 2023

+919-534

Commits

Commits on Jul 20, 2023

• glmmseq convert cat into message

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• Merge branch 'dev' of github.com:stemangiola/tidybulk into dev

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• glmmseq convert cat into message

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• Merge branch 'dev' of github.com:stemangiola/tidybulk into dev

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• add tibble methods

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• add SE methods

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Commits on Jul 21, 2023

• fix tests

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• gitignore

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  d0c6186

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• fix tests

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  b8dfd54

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• fix test

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Commits on Jul 23, 2023

• make multiple column more robust

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Commits on Jul 24, 2023

• fix vignette

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• fix documentation

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  e3a8b79

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• fix tests

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  be2dac6

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• drop tests for combat_seq

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  7d0d68e

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• fix combat_seq for SE

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  c2545c0

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• fix test for mac, increase tollerance

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  7d49bf7

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• Merge pull request #281 from stemangiola/add-combatSeq

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• modify test to allow tidy mutate

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• fix bug

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Commits on Jul 27, 2023

• Merge pull request #284 from stemangiola/allow-tidy-expression-in-test_gene_overrepresentation

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Commits on Aug 22, 2023

• add argument

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Commits on Aug 23, 2023

• make sure matrix is maintained when selecting rows

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Commits on Aug 28, 2023

• allow one gene for DE

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• Update check-bioc.yml

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Commits on Aug 29, 2023

• Revert "Update check-bioc.yml"

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• add argument

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  23666f4

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• make sure matrix is maintained when selecting rows

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  898918e

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• allow one gene for DE

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  3aeee9a

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• Merge branch 'custom-dispersion-DE' of https://github.com/stemangiola/tidybulk into custom-dispersion-DE

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• Merge pull request #283 from stemangiola/dev

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• drop dataset

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  3cbb3d2

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• add dispersion to tibble input for glmmseq

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  fca9009

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• remove library

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  318be24

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• update tests

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  22457ec

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• fix tests

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  d0b66de

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• fix tests

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  14b8cd1

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• drop deseq2 object

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  69b5dfa

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• Merge pull request #289 from stemangiola/avoid-hard-dependency-with-deseq2

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• add argument

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  9c8c787

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• make sure matrix is maintained when selecting rows

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  80bc670

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• allow one gene for DE

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  3129127

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• add dispersion to tibble input for glmmseq

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  a177945

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• Merge branch 'custom-dispersion-DE' of https://github.com/stemangiola/tidybulk into custom-dispersion-DE

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  d56afc0

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• add custom dispersion for tibble input

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