Changes in version 0.5.0                        

  - The multiOmicDataSet class has been moved to a new package,
    MOObject. (#277, @kelly-sovacool)
      - Ensure backward compatibility by coercing legacy MOSuite MOO
        objects when read/loaded. (#281, @kelly-sovacool)
  - Harmonize Volcano Plot output dimensions as physical inches with 300
    DPI defaults for Enhanced and Summary plots. (#274, @TJoshMeyer)

                        Changes in version 0.4.2                        

  - Align Volcano Plot threshold comparisons across labeling, coloring,
    and summary filtering, and use resolved column names for
    classification. (#266, @TJoshMeyer)
  - normalize_counts() now uses normalized counts instead of filtered
    counts for the correlation heatmap so it matches the PCA and
    histogram outputs. (#269, @phoman14)

                        Changes in version 0.4.1                        

  - Fix how plot_volcano_summary() & plot_volcano_enhanced handle
    detecting column names for features, significance, and fold-change.
    plot_volcano_summary() plot now uses plot_volcano_enhanced() for
    rendering. (#239, @phoman14)

                        Changes in version 0.4.0                        

  - Update PCA label, point-size, and histogram behavior. (#230,
    @phoman14)
  - Add optional count log-transform controls for PCA plots. (#234,
    @phoman14)
  - Add a post-clean CPM histogram output in clean_raw_counts(). (#234,
    @phoman14)
  - Improvements to plot colors: (#223, @phoman14)
      - Align plot color defaults with the MOSuite Code Ocean capsule
        defaults while preserving fallback random colors when a
        requested palette is too short.
      - Improve top and bottom legend wrapping and automatic legend text
        sizing for PCA and histogram plots with many or long labels.
      - Add optional group coloring to plot_read_depth() and the
        clean_raw_counts() read-depth output while preserving the
        single-color default when no group is selected.
  - New function display_colors() shows a multiOmicDataSet's chosen
    color palettes, and get_colors_lst() now takes a palette vector
    rather than function for simplicity. (#236, @kelly-sovacool)
  - New report template & helper function: render_report(). (#120,
    @kelly-sovacool)
  - Fix ggplot2 size deprecation warning in plot_volcano_summary().
    (#228, @kelly-sovacool)
  - docs: show how to set output_dir in render_report(). (#235,
    @kelly-sovacool)

                        Changes in version 0.3.2                        

  - Support ggplot2 v4.0.0 for correlation heatmap plots in
    filter_counts(), normalize_counts(), and batch_correct_counts().
    (#205, @copilot, @kelly-sovacool)

                        Changes in version 0.3.1                        

  - Fix recursion error in plot_venn_diagram(). (#188, @kelly-sovacool)
  - Fix S7 dispatch argument mismatch in plot_read_depth() and
    plot_histogram(). (#200, @copilot, @kelly-sovacool)
  - Fix bug in remove_low_count_genes() when use_group_based_filtering =
    TRUE. (#200, @copilot, @kelly-sovacool)
  - Fix color palette selection to fall back to random colors with a
    message when the number of categories exceeds the palette maximum.
    (#204, @copilot, @kelly-sovacool)
  - Update S7 class, generic, and method documentation to use roxygen2
    v8.0.0. (#206, #212, @copilot, @kelly-sovacool)
  - A docker container with only MOSuite's dependencies, not MOSuite
    itself, is now available:
    https://hub.docker.com/r/nciccbr/mosuite-minimal. (#209,
    @kelly-sovacool)
  - Minor bug fixes in calc_cpm_df(),
    create_multiOmicDataSet_from_dataframes(), and diff_counts()
    docstring. (#214, @kelly-sovacool)

                        Changes in version 0.3.0                        

New features

  - New function write_multiOmicDataSet_properties(). (#173,
    @kelly-sovacool)
      - Extracts all the properties from a multiOmicDataSet and writes
        any data frames as csv files, other objects are written as rds
        files.
  - New utility functions to reduce code duplication across Code Ocean
    capsules: (#185, @kelly-sovacool) setup_capsule_environment(),
    load_moo_from_data_dir(), parse_optional_vector(),
    parse_vector_with_default(), and parse_samples_to_rename().

Bug fixes

  - Fixed bug in clean_raw_counts() where duplicate gene rows were not
    being aggregated correctly. (#162, @TJoshMeyer)
  - Fixed batch_correct_counts() to gracefully skip batch correction
    when only a single batch level exists; the function now warns
    without erroring. (#158, @TJoshMeyer)
  - Fixed multiOmicDataSet validator to return character vector instead
    of using stop() per S7 documentation. (#177, @copilot,
    @kelly-sovacool)
  - Fixed duplicate PCA figure files in filter_counts(),
    normalize_counts(), and batch_correct_counts(). (#180,
    @kelly-sovacool)
  - Bug fixes: (#174, @kelly-sovacool)
      - Fixed bugs in plot_volcano_summary(), plot_volcano_enhanced(),
        and plot_pca_3d() when used with multiOmicDataSet objects.
      - Fixed bug in filter_diff() when filtering_mode = "all" that was
        causing plot rendering errors.
      - Fixed plot_pca_2d() to save plots to disk correctly.
  - Replaced deprecated arrange_() with arrange() in
    plot_expr_heatmap(). (#182, @kelly-sovacool)
  - Improvements for use with Galaxy. (#168, #170, #171, #174,
    @kelly-sovacool)

                        Changes in version 0.2.1                        

  - A docker image is now available. (#134)
      - https://hub.docker.com/r/nciccbr/mosuite
  - Minor documentation improvements. (#135)
  - Improvements for use with Galaxy. (#149)
  - Fixed bug where 3D PCA plots were not being saved. (#149)

                        Changes in version 0.2.0                        

  - Any user-facing function can now be called from the unix command
    line to support Galaxy. (#126, #127) Usage: mosuite [function]
    --json=path/to/args
      - It is not recommended for most users to run MOSuite via the CLI;
        this is only intended for the Galaxy workflow.
  - MOSuite is now archived in Zenodo with a DOI:
    10.5281/zenodo.16371580

                        Changes in version 0.1.0                        

This is the first release of MOSuite 🎉

  - Note: at the start of development, this package was called
    reneeTools. Later it was renamed to MOSuite. (#76)

Main functions & classes

  - multiOmicDataSet (#16, #28)
      - create_multiOmicDataSet_from_files()
      - create_multiOmicDataSet_from_dataframes()
  - run_deseq2()
  - calc_cpm() (#38)
  - filter_counts() (#38)
  - clean_raw_counts() (#79)
  - normalize_counts() (#82)
  - batch_correct_counts() (#87)
  - diff_counts() (#102)
  - filter_diff() (#110)

visualization

  - plot_histogram() (#96)
  - plot_corr_heatmap() (#96)
  - plot_expr_heatmap() (#90, #96)
  - plot_pca() (#88, #96)
  - plot_volcano_enhanced() (#112)
  - plot_volcano_summary() (#112)
  - plot_venn_diagram() (#111)

vignettes

  - intro
  - visualization
  - memory
  - renee