Changes in version 1.1.3                        

  - Vignettes
      - added examples on pltOvrHm()
      - added pseudocode for MPAC
      - changed MPAC's full name

                        Changes in version 1.1.2                        

  - pltOvrHm(): use lowercase 'p' instead of 'P' in heatmap colorbar
    legend
  - MPAC's full name is changed to 'Multi-omic Pathway Analysis of Cell'

                        Changes in version 1.1.1                        

  - added new functions
      - pltOvrHm(): to plot a heatmap of over-represented gene sets for
        clustered samples
      - ppRunPrd(): to prepare required files to run PARADIGM
  - updated existing functions
      - conMtf(): use decompose() instead of decompose.graph() for
        igraph 2.0
      - ppPermInp(): increased default permutations from 3 to 100
      - ppRealInp() and ppRnaInp(): added an option rna_n_sd to set
        standard deviation range to define RNA state
      - pltNeiStt(): fixed bugs and adjusted output figure height
      - colPermIPL() & fltByPerm(): added a threads option to
        parallelize
      - runPrd() & runPermPrd(): when no sampleids is provided, all the
        samples in input real_se and perml will be used.
      - subNtw(): entities with NA values in all samples in the input
        fltmat will be ignored.
  - updated tests
      - test-conMtf() & test-subNtw(): use as_edgelist() instead of
        get.edgelist() for igraph 2.0
      - test-conMtf() & test-ovrGMT(): add upgrade_graph() on extdata

                       Changes in version 0.99.10                       

Added documentation in inst/scripts/ for the source and derivation of
inst/extdata/

                       Changes in version 0.99.1                        

  - Used SummarizedExperiment objects for CNA and RNA matrix in
    functions:
    
      - ppCnInp()
      - ppRnaInp()
      - ppPermInp()
      - runPrd()
      - runPermPrd()
      - pltNeiStt()

  - Added a function to prepare both CNA and RNA input: ppRealInp()

  - Removed GitHub PARADIGM URLs from R code

  - Removed dependence on the magrittr package

                       Changes in version 0.99.0                        

  - Added a NEWS.md file to track changes to the package.