Changes in version 1.5.2                        

Summary

  - Added additional columns in TFinfluence output that describe the
    availabilty of the TF and its mutation in MAVISp

                        Changes in version 1.5.1                        

Summary

  - Added TFinfluence function, that implements a secondary layer that
    checks the influence of destabilizing mutations on transcription
    factors as mechanistic explanation for expression changes

                        Changes in version 1.5.0                        

Summary

  - version bump due to release of Bioconductor 3.20

                        Changes in version 1.3.0                        

Summary

  - version bump due to release of Bioconductor 3.19

                        Changes in version 1.1.2                        

Summary

  - fixed issue with parallelization in URA

                        Changes in version 1.1.1                        

Summary

  - added new functionality called GMA (Gene Methylation Analysis)
  - added three new visualization functions in connection with GMA:
    plotGMA, plotMoonlightMet, plotMetExp
  - updated vignette to contain new functionalities related to GMA
  - updated class testing in all functions
  - resized figures

                       Changes in version 0.99.14                       

Summary

  - made test for GRN and arm64 less stringent to account for
    architectural differences

                       Changes in version 0.99.13                       

Summary

  - refactored examples to make them faster

                       Changes in version 0.99.12                       

Summary

  - added data loadings in functions

                       Changes in version 0.99.11                       

Summary

  - added missing data loadings in vignette
  - changed handling of null cases in PRAToTibble

                       Changes in version 0.99.10                       

Summary

  - updated code style in all functions

                       Changes in version 0.99.9                        

Summary

  - fixed hardcoded plot title in plotFEA
  - updated reference in docs to published paper
  - fixed excessively long example line in GLS function
  - moved globalVariables calls after function definitions
  - turned LazyData to false and issued connected fixes

                       Changes in version 0.99.8                        

Summary

  - replaced number sequences generation (e.g. using seq(n) instead of
    1:n) in all functions

                       Changes in version 0.99.7                        

Summary

  - added bindings for global variables in majority of functions

                       Changes in version 0.99.6                        

Summary

  - switched \dontrun to \donttest in some examples

  - fixed vignette to have fewer eval=FALSE chunks

                       Changes in version 0.99.5                        

Summary

  - added several checks for correctness of main function arguments

                       Changes in version 0.99.4                        

Summary

  - changed instances of sapply to vapply

                       Changes in version 0.99.3                        

Summary

  - added tests with testthat

  - updated following example data: dataFEA, dataGRN, dataURA, dataPRA
    and cscape_somatic_output

  - added following example data: dataURA_plot, dataGRN_no_noise

                       Changes in version 0.99.2                        

Summary

  - added GLS (Gene Literature Search) function

  - fixed library problems with vignettes

                       Changes in version 0.99.1                        

Summary

  - removed package documentation from Rdata.R

                       Changes in version 0.99.0                        

Summary

  - first release of Moonlight2R.

New features (added or significantly changed respect to MoonlightR)

  - DMA			Driver mutation analysis

  - plotDMA		Creates one or more heatmap of the output from DMA

  - plotMoonlight	Creates heatmap of Moonlight Gene Z-scores for
    selected genes

  - EncodePromoters	Experimentially verified promoter sites

  - LOC_protein		Level of consequence protein

  - LOC_translation	Level of consequence translation

  - LOC_transcription	Level of consequence transcription

  - NCG			Network of Cancer Genes 7.0

  - dataPRA		output from PRA function

  - dataMAF		Mutation data from TCGA-LUAD

  - dataDMA		Output from DMA function

  - cscape_somatic_output	Cscape-somatic annotations of TCGA-LUAD

  - DEG_Mutations_Annotations	Differentially expressed genes's Mutations

  - Oncogenic_mediators_mutation_summary	Oncogenic Mediators Mutation
    Summary

  - moonlight		Function to run moonlight pipeline