# Moonlight2R 1.9.4

## Summary

* Made p-value tests for FEA(method='fgsea') more qualitative to address low reproducibility of gfsea()

# Moonlight2R 1.9.3

## Summary

* Fixed tests for FEA with "fgsea" as method and added new parameter ('seed') to the FEA() function for setting random seed and control stochastic perumation-based fgsea scores and p-values.

# Moonlight2R 1.9.2

## Summary

* Added new dataset for proteomics data and implemented fgsea method in the FEA function

# Moonlight2R 1.9.1

## Summary

* Removed hotfix in GSEA() module

# Moonlight2R 1.9.0

## Summary

* Updated version for BioC release

# Moonlight2R 1.7.4

## Summary

* Updated GLS() and GMA() examples to reduce the check timings

# Moonlight2R 1.7.3

## Summary

* fixed error in GSEA() module due to issues in DOSE package devel version

# Moonlight2R 1.7.2

## Summary

* fixed error in plotDMA and other plotting functions due to updates in tidyHeatmap package

# Moonlight2R 1.7.1

## Summary

* fixed error in GLS function due to updates in easyPubMed package

# Moonlight2R 1.7.0

* version bump due to release of Bioconductor 3.21

# Moonlight2R 1.5.5

## Summary

* fixed mistake in the documentation of the `TFinfluence` function

# Moonlight2R 1.5.4

## Summary

* added missing documentation file

# Moonlight2R 1.5.3

## Summary

* Filter only missense mutations of MAF in TFinfluence.
* Switched to RaSp/FoldX consensus as a default of MAVISp in TFinfluence.
* Corrected the code of 'mutation_available' column of TFinfluence output
to correctly check the presence of the mutation in MAVISp data.

# Moonlight2R 1.5.2

## Summary

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

# Moonlight2R 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

# Moonlight2R 1.5.0

## Summary

* version bump due to release of Bioconductor 3.20

# Moonlight2R 1.3.0

## Summary

* version bump due to release of Bioconductor 3.19

# Moonlight2R 1.1.2

## Summary

* fixed issue with parallelization in URA

# Moonlight2R 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

# Moonlight2R 0.99.14

## Summary

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

# Moonlight2R 0.99.13

## Summary

* refactored examples to make them faster

# Moonlight2R 0.99.12

## Summary

* added data loadings in functions

# Moonlight2R 0.99.11

## Summary

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

# Moonlight2R 0.99.10

## Summary

* updated code style in all functions

# Moonlight2R 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

# Moonlight2R 0.99.8

## Summary

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

# Moonlight2R 0.99.7

## Summary

* added bindings for global variables in majority of functions

# Moonlight2R 0.99.6

## Summary

* switched `\dontrun` to `\donttest` in some examples

* fixed vignette to have fewer `eval=FALSE` chunks

# Moonlight2R 0.99.5

## Summary

* added several checks for correctness of main function arguments

# Moonlight2R 0.99.4

## Summary

* changed instances of `sapply` to `vapply`

# Moonlight2R 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

# Moonlight2R 0.99.2

## Summary

* added `GLS` (Gene Literature Search) function

* fixed library problems with vignettes

# Moonlight2R 0.99.1

## Summary

* removed package documentation from Rdata.R

# Moonlight2R 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
