Open-Hotgenes/NEWS at main · pfizer-opensource/Open-Hotgenes · GitHub

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# version 0.0.54:
    - Replaced base R messaging/error calls (stop(), warning(), message(),
      print(), cat()) with cli equivalents across R/ sources.
    - Added verbose arg to fgsea_() to control contrast name logging;
      defaults to FALSE.
    - Added contrast_vectors arg to HotgenesDEseq2() to support
      contrast setting.

# version 0.0.53:
    - Added Build_DILI_Hotgenes.R to data-raw — builds a Hotgenes object
      from the publicly available DILI discovery proteomics dataset
      (Federspiel et al., MassIVE MSV000089782).
    - Other clean up

# version 0.0.52:
    - Exported make_stat_frame()
    - Cleaned up documentation in Venn methods.

# version 0.0.51:
    - Added make_stat_frame() to support ranks stats clustering methods
      via FactoWrapper_DFs().
    - Dropped SamplesIDs arg for FactoWrapper_DFs(), which now
      requires rownames.
    - Added plot_type arg to factoExtra_DFs(), which now supports
      biplots and ind plots using factoextra.

# version 0.0.50:
    - Added news to shiny app.

# version 0.0.49:
    - Added console message to inform number of overlapping
      features between ranks and genesets to fgsea_()
    - New modal for shiny fgsea tab alert you when there's no overlap
      between you input ranks and selected geneset params.
    - msigdbr_wrapper() now supports multiple set values.
    - Mapper_() now returns all columns as charater.

# version 0.0.48:
    - Updated Heatmap with default aliases
    - Changed behavior of annotateSig for DE(), which now always annotates
      significance when TRUE and not just when a hot list is provided.

# version 0.0.47:
    - Added alias mapping support for cluster passed from PCA tab to fgsea
      tab in app.
    - Aliases now included in TopTibble slot from PCA output
    - Added the ability to set levels for heatmap annotations

# version 0.0.46:
    - Added legend_text_size to factoExtra_DFs() and to shiny app

# version 0.0.45:
    - Dropped NaN detection

# version 0.0.44:
    - Added NaN detection to detected_missinginess and related functions.

# version 0.0.43:
    - Added support for imputing rank values for gsea
    - Added keep_na_padj arg to utilities for supporting the export of
      DE results, which can be useful if some padj values are NA
    - Updated the shiny app to now include an features with NA in padj column
      when downloading unfiltered results

# version 0.0.42:
    - Added HotgenesDRomics()

# version 0.0.41:
    - Added improved missing data checks with all_truthy(),
      any_missingness(), any_truthy(), and detected_missingness().
    - Improved na_check(), which now trims white spaces before checking
      for NA, "", and "NA"

# version 0.0.40:
    - Added min_col_levels to coldata_() and set to 0

# version 0.0.39:
    - Added min to internal df_coldata_handler and set to 0
    - Updated msigdbr_wrapper() to use 'collection'

# version 0.0.38:
    - Updated to work with latest version of msigdbr

# version 0.0.37:
    - Updated HotgeneSets() methods for GSVA (>= 1.50.0)

# version 0.0.36:
    - Fixed ... arg bug for HotgeneSets()

# version 0.0.35:
    - Added support for precision weights for geneset sizes
    - Added use_weights and use_vooma args to HotgeneSets()

# version 0.0.34:
    - Modularized HotgeneSets() function with internal Hotgsva()
    - Added wrap_fixed_names() to wrap names that have been cleaned

# version 0.0.33:
    - Added additional support function for supplying custom genesets
    - Fixed bug in msig_wrapper

# version 0.0.32:
    - Fixed max_col_levels bug in Shiny_Hotgenes()
    - Changed set the default for max_col_levels to Inf

# version 0.0.31:
    - Changed R 4.3 requirement to R 4.2; however, HotgeneSets() functionality will only work for R 4.3+

# version 0.0.30:
    - Added HotgeneSets name checks and fixes (with a warning)
    - HotgeneSets includes a "size" column in the Mapper slot, which represents
      the geneset size.
    - Added "Subset" button to shiny expression plot tab
    - Added "Hotlist" tab to DE stats tab, which shows details for select features

# version 0.0.29:
    - Added log2fc cut off to PCA tab
    - Also fixed sidepanel conditional panel issue

# version 0.0.28:
    - Added support for alias labeling in shiny app.
    - Alias selection is available via the names_col arg in ExpsPlot()
    - Mapper_() now limits cols by minimum number of distinct values.
    - Cleaned up some of the shiny code

# version 0.0.27:
    - Moved logo in app
    - Set the default tab to "BoxPlot" for app loading
    - Some clean up
    - Brought back repel labels for volcano plot in shiny app

# version 0.0.26:
    - Added Hotgenes_logo support

# version 0.0.25:
    - Cleaned up readme and converted to .Rmd format
    - Added pkgdown website
    - ran usethis::use_apl2_license()