Changes in version 1.5.4
Summary
- added missing documentation file
Changes in version 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.
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