Changes in version 1.3.5                        

Bioconductor preparation

  - Added biocViews to DESCRIPTION.
  - Added BiocStyle vignette.
  - Updated R dependency to >= 4.4.0.
  - Added @return tags to all exported functions.
  - Fixed typos in documentation.
  - Replaced class(x) %in% with is.numeric().
  - Converted NEWS to NEWS.md format.

                       Changes in version 1.0-39                        

  - parseDesignContrast adds new parameter expSampleNames to allow
    sample name consistency check with input matrix.

                       Changes in version 1.0-34                        

  - DesignContrast prints error message if validity is violated.
  - parseDesignContrastFile fixes a mistake of assigning group levels.
  - parseDesignContrastFile now accepts the dispLevelStr option.

                       Changes in version 1.0-33                        

  - parseDesignContrastStr fixes two errors.

                       Changes in version 1.0-32                        

  - Add DesignContrast object.

                       Changes in version 1.0-29                        

  - Add new functionality in keepMaxMeanProbes.Rscript: able to read
    from .CHIP file.
  - keepMaxMeanProbes.Rscript now does not depend on the S4 class
    ExpressionSet anymore, therefore much faster.

                       Changes in version 1.0-28                        

  - Debug keepMaxMeanProbes.Rscript: extname returns NA if not found,
    therefore an additional check is added.

                       Changes in version 1.0-27                        

  - Function extension in ChipFetcher2ExpressionSet: now non-Affymetrix
    probesets are supported as well.

                       Changes in version 1.0-26                        

  - The main body of readCls has been moved to ribiosIO::read_cls.
    readCls becomes a synonym for compatibility.

                       Changes in version 1.0-25                        

  - Improvement in readCls: error messages provide more informative
    details for mal-formatted files.

                       Changes in version 1.0-24                        

  - Bug fix in writeEset: expression matrix is written without quotes.
  - New script: keepMaxMeanProbes.Rscript filters duplicated genes by
    taking the one with maximum average expression.

                       Changes in version 1.0-23                        

  - Bug fix in readGct: if input feature names have duplicates, the
    exprs matrix row names are changed.

                       Changes in version 1.0-22                        

  - Move exprsMat2gct.Rscript to the ribiosIO package.
  - writeGct has been refactored for matrix in ribiosIO, and
    re-implemented as an S4-method for matrix and ExpressionSet.

                       Changes in version 1.0-21                        

  - Add exprsMat2gct.Rscript to convert between expression matrix files
    and GCT files.

                       Changes in version 1.0-20                        

  - ChipFetcher2ExpressionSet: add option orthologue.
  - keepMaxStatProbe uses function(x) mean(x, na.rm=TRUE) as default
    function.

                       Changes in version 1.0-19                        

  - limma2gsea.Rscript is updated.

                       Changes in version 1.0-18                        

  - Refactor GSEA-related functions that are not dependent on the
    Biobase data structure to the ribiosGSEA package.

                       Changes in version 1.0-17                        

  - limma2gsea.Rscript guarantees no replicated gene symbols after
    orthologue mapping.

                       Changes in version 1.0-16                        

  - Add limma2gsea.Rscript to inst/Rscript.

                       Changes in version 1.0-15                        

  - The ribiosAnnotation package has been removed from the dependency
    list.
  - Add comp_diff.Rscript to inst/Rscript.

                       Changes in version 1.0-14                        

  - The deprecation message of remainHighestVarProbe and
    keepHighestVarProbe have been updated.

                       Changes in version 1.0-13                        

  - The rowscale method warns if the input ExpressionSet does not have
    'lockedEnvironment' as storageMode.

                       Changes in version 1.0-12                        

  - Low-level functions for computational drug repositioning refactored
    into ribiosReposition.

                       Changes in version 1.0-11                        

  - Add feature in summarizeProbesets: option keep.featureNames.
  - Rename and rewrite sprintGmt to formatGmt as S4 method.

                       Changes in version 1.0-10                        

  - Bugfix in readEset for numeric column names.
  - Add annotate and reannotate methods.
  - Add documentation for the ribios.ExpressionSet object.

                        Changes in version 1.0-9                        

  - Add kendallW function and kendallWmat S4-method.

                        Changes in version 1.0-8                        

  - PCA-related data structures and functions are refactored into the
    ribiosPCA package.

                        Changes in version 1.0-7                        

  - Add summarizeProbesets to summarize probesets.
  - NAMESPACE are now explicitly stated.

                        Changes in version 1.0-6                        

  - Add dependency on the ribiosAnnotation package.
  - Add writeEset and readEset functions.
  - readFKdata was renamed as readFKtable.

                        Changes in version 1.0-5                        

  - Add git version control.

                        Changes in version 1.0-4                        

  - Move data.frame and matrix functions to the ribiosUtils package.

                        Changes in version 1.0-3                        

  - Refactor read_gct into ribiosIO for efficiency.

                        Changes in version 1.0-2                        

  - Change keepHighestVarProbe to more generalized keepMaxStatProbe.

                        Changes in version 1.0-1                        

  - Remove the path option from the readGctCls function.