NEWS

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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