Changes in version 1.9.1                        

  - Corrected a bug in positiveQC(), which caused it to calculate
    different positive scale factors from normalize_pos_control(); the
    second was confirmed to be correct.

                        Changes in version 1.7.2                        

  - runLimmaAnalysis now allows optional arguments, which are passed to
    limma::lmFit.

                        Changes in version 1.7.1                        

  - The codeclass.retain option now allows runLimmaAnalysis() to be run
    using a CodeClass/CodeClasses specified by the user, instead of
    automatically removing non-endogenous genes. See
    help(runLimmaAnalysis) for details.
  - processNanostringData() can now handle a vector of .rcc files, in
    addition to the previous options for loading NanoString data.

                        Changes in version 1.5.1                        

  - We're published in Bioinformatics! CITATION file updated.

                        Changes in version 1.3.7                        

  - In addition to ruv::RUVIII, the RUVSeq::RUVg method can now be used
    for data normalization. Options have also been added to allow tuning
    of the parameters for these methods. More details are provided in
    the vignette.
  - A csv or txt file containing a design matrix can be input as a
    'sampleTab' in processNanostringData(). This facilitates easier
    differential expression analysis with more complex models, and an
    example has been added to the vignette.
  - Various other improvements to vignette.

                        Changes in version 1.3.6                        

  - NanoTube can now process zipped and tarred (.zip or .tar)
    directories, as well as gzipped (.gz) RCC files, such as those
    downloaded from GEO in many cases.

                        Changes in version 1.3.5                        

  - Corrected a bug that caused NanoTube not to recognize reporters
    labeled as "Endogenous1", "Endogenous2", etc. as Endogenous.

                        Changes in version 1.1.2                        

  - When processing a folder containing RCC files,
    processNanostringData() now ignores filenames not ending in "RCC"
    (case-insensitive).
  - Corrected a bug that in read_cpdb_sourceDBs() and read_cpdb_tab()
    that sometimes led to the data being misread.

                       Changes in version 0.99.0                        

  - Pre-release version