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development version

  • Fix recursion error in plot_venn_diagram(). (#188, @kelly-sovacool)

MOSuite 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)

MOSuite 0.2.1

  • A docker image is now available. (#134)
  • Minor documentation improvements. (#135)
  • Improvements for use with Galaxy. (#149)
  • Fixed bug where 3D PCA plots were not being saved. (#149)

MOSuite 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

MOSuite 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