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Add conditional print method for objects that contain alternative experiments #89

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Add conditional print method for objects that contain alternative experiments #89

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Commits on Aug 23, 2023

  1. test change print_method.R

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  2. Update print_method.R

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  3. Update print_method.R

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  4. Update print_method.R

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Commits on Aug 27, 2023

  1. Update print_method.R

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Commits on Aug 28, 2023

  1. Update print_method.R

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  2. Update print_method.R

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  3. Update print_method.R

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  4. Update print_method.R

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  5. Update print_method.R

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  6. Update print_method.R

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  7. Update print_method.R

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Commits on Aug 29, 2023

  1. Update print_method.R

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  3. Update print_method.R

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  4. Update print_method.R

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  5. Update test-methods.R 

    Add show test for alt experiments
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  6. Update test-methods.R 

    Add test
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Commits on Aug 30, 2023

  1. Update test-methods.R 

    New, more comprehensive unit tests
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Commits on Sep 1, 2023

  1. Update utilities.R 

    Add altExp functionality to `get_abundance_sc_wide` and `get_abundance_sc_long`.
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Commits on Sep 2, 2023

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Commits on Sep 9, 2023

  1. Update utilities.R 

    Split out functions
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  2. Update methods.R 

    Add altExp functionality to aggregate_cells
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  3. Update methods.R 

    Tweak to aggregate_cells
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  4. Update methods.R 

    Tweak aggregate_cells
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  5. Update test-methods.R

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  7. Merge branch 'master' into altExp_methods

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Commits on Sep 27, 2023

  1. Update utilities.R 

    update `get_abundance_sc_long` to allow multiple assays
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  2. Update utilities.R 

    update to assay selection
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  3. Update utilities.R 

    dealing with assays specification
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  4. Update utilities.R 

    Amend get_abundance_sc_wide
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  5. Update methods.R 

    Tweak join_features
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  6. Update methods.R

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  7. Update utilities.R

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  11. Update methods.R

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  12. Update methods.R

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  13. Update methods.R

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  25. Update methods.R

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  27. Update utilities.R 

    Solve name_repair issue
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  28. Update methods.R

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  29. Update utilities.R

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  30. Update utilities.R

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  31. Update dplyr_methods.R

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  32. Update dplyr_methods.R

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  33. Update utilities.R

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  34. Update utilities.R

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Commits on Sep 29, 2023

  1. Update methods.R

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Commits on Sep 30, 2023

  1. Update methods.R 

    Fix aggregate cells
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  1. Update utilities.R

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  3. Update test-methods.R

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Commits on Oct 19, 2023

  1. Merge branch 'stemangiola:master' into altExp_methods

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  2. Update utilities.R

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  3. Update utilities.R

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Commits on Oct 20, 2023

  1. Update utilities.R

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  4. Update utilities.R 

    Trying all features
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  5. Update utilities.R 

    Tweak to allow specific assays
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  6. Update utilities.R 

    Should capture all possible assay specifications now
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  7. Update utilities.R 

    Tweak wide to account for features that have the same name in multiple assays
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Commits on Oct 23, 2023

  1. Update methods.R 

    new aggregate_cells
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Commits on Oct 25, 2023

  1. Update methods.R 

    Add SummarizedExperiment as output
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  1. Update methods.R 

    Try coercing into a SummarizedExperiment object
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  2. Update test-methods.R 

    Add altExp optionality to the unit test for aggregate_cells
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Commits on Nov 1, 2023

  1. Update methods.R 

    Fix feature_original and add comments to code blocks.
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  7. Update introduction.Rmd 

    Add assays for shape="wide"
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  8. Update introduction.Rmd

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  4. Update methods.R

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  5. Update methods.R

    @Biomiha
    Biomiha authored Nov 3, 2023
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  6. Update test-ggplotly_methods.R

    @Biomiha
    Biomiha authored Nov 3, 2023
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Commits on Nov 9, 2023

  1. Update test-methods.R

    @Biomiha
    Biomiha authored Nov 9, 2023
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  2. Update plotly_methods.R

    @Biomiha
    Biomiha authored Nov 9, 2023
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Commits on Nov 12, 2023

  1. Update plotly_methods.R

    @Biomiha
    Biomiha authored Nov 12, 2023
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  2. Merge branch 'master' into altExp_methods

    @Biomiha
    Biomiha authored Nov 12, 2023
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Commits on Dec 6, 2023

  1. Merge branch 'master' into rebase-solve-conflicts

    @stemangiola
    stemangiola authored Dec 6, 2023
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Commits on Jan 1, 2024

  1. Merge plot_ly to work

    @Biomiha
    Biomiha committed Jan 1, 2024
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  2. Merge pull request #1 from stemangiola/rebase-solve-conflicts 

    rebase
    @Biomiha
    Biomiha authored Jan 1, 2024
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  3. delete unnecessary plot

    @Biomiha
    Biomiha committed Jan 1, 2024
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  4. Merge branch 'master' into altExp_methods

    @Biomiha
    Biomiha committed Jan 1, 2024
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  5. add error handling in yaml

    @Biomiha
    Biomiha committed Jan 1, 2024
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  6. add CMD check

    @Biomiha
    Biomiha committed Jan 1, 2024
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Commits on Jan 3, 2024

  1. Update methods.R 

    small tweaks
    @Biomiha
    Biomiha authored Jan 3, 2024
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Commits on Feb 3, 2024

  1. Minor bug fixes to utilities

    @Biomiha
    Biomiha authored Feb 3, 2024
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Commits on Feb 4, 2024

  1. Replace deprecated function when with if else statements

    @Biomiha
    Biomiha authored Feb 4, 2024
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  2. Update methods.R 

    Remove importFrom dplyr::bind_rows
    @Biomiha
    Biomiha authored Feb 4, 2024
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  3. Update utilities.R 

    Remove importFrom `when`
    @Biomiha
    Biomiha authored Feb 4, 2024
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  4. Sync abundance functions with master repo

    @Biomiha
    Biomiha authored Feb 4, 2024
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  5. Sync with master repo

    @Biomiha
    Biomiha authored Feb 4, 2024
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  6. Correct variables_genes issue

    @Biomiha
    Biomiha authored Feb 4, 2024
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  7. Sync with master repo

    @Biomiha
    Biomiha authored Feb 4, 2024
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  8. Sync with master repo

    @Biomiha
    Biomiha authored Feb 4, 2024
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  9. Merge branch 'master' into altExp_methods

    @Biomiha
    Biomiha authored Feb 4, 2024
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  10. Correct unique features

    @Biomiha
    Biomiha authored Feb 4, 2024
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Commits on Feb 6, 2024

  1. Can it pass checks?

    @Biomiha
    Biomiha committed Feb 6, 2024
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Commits on Feb 11, 2024

  1. Merge branch 'stemangiola:master' into altExp_methods

    @Biomiha
    Biomiha authored Feb 11, 2024
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  2. Add files via upload

    @Biomiha
    Biomiha authored Feb 11, 2024
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  3. Remove MASS import requirement

    @Biomiha
    Biomiha authored Feb 11, 2024
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  4. Add n_extra desc

    @Biomiha
    Biomiha authored Feb 11, 2024
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Commits on Feb 18, 2024

  1. Update tibble_methods.R

    @Biomiha
    Biomiha authored Feb 18, 2024
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  2. testthat methods

    @Biomiha
    Biomiha committed Feb 18, 2024
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