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fix: add more logging statemens to sleuth-diffexp.R, add QuantSeq testing data to get QuantSeq tests to pass #86

Merged
merged 12 commits into from
Jan 29, 2024
Merged

fix: add more logging statemens to sleuth-diffexp.R, add QuantSeq testing data to get QuantSeq tests to pass #86

merged 12 commits into from
Jan 29, 2024

Commits on Jan 11, 2024

  1. debugging statement at estimated vroom error spot

    @dlaehnemann
    dlaehnemann committed Jan 11, 2024
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Commits on Jan 16, 2024

  1. add logging statements in write_results function of sleuth-diffexp.R

    @dlaehnemann
    dlaehnemann committed Jan 16, 2024
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  2. add logging statement for loading custom representative transcripts f… 

    …ile in sleuth-diffexp.R
    @dlaehnemann
    dlaehnemann committed Jan 16, 2024
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  3. fix: remove non-existant column canonical from genes_aggregated datav… 

    …zrd output
    @dlaehnemann
    dlaehnemann committed Jan 16, 2024
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Commits on Jan 18, 2024

  1. remove debugging dump statement, so we can merge added logging statem… 

    …ents back into main PR branch
    @dlaehnemann
    dlaehnemann committed Jan 18, 2024
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Commits on Jan 26, 2024

  1. feat: change QuantSeq test to use curated testing data set

    @dlaehnemann
    dlaehnemann committed Jan 26, 2024
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  2. use cli_abort instead of stop

    @dlaehnemann
    dlaehnemann committed Jan 26, 2024
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  3. snakefmt

    @dlaehnemann
    dlaehnemann committed Jan 26, 2024
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  4. remove recursive checkout of ngs-test-data submodule for three-prime … 

    …test
    @dlaehnemann
    dlaehnemann committed Jan 26, 2024
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  5. use all available cores in CI tests

    @dlaehnemann
    dlaehnemann committed Jan 26, 2024
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Commits on Jan 29, 2024

  1. fix: newer org.Hs.eg.db versions seem to have gene symbols in all cap… 

    …s, as is usual, so no more str_to_title() conversion is needed in the fgsea.R script
    @dlaehnemann
    dlaehnemann committed Jan 29, 2024
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  2. fix: add library(data.table) and data.table() conversion in fgsea::co… 

    …llapsePathways() to avoid ctlab/fgsea#98
    @dlaehnemann
    dlaehnemann committed Jan 29, 2024
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