maftools: Summarize, Analyze and Visualize MAF Files

CHANGES IN VERSION 2.4.05

Highlight most significant entry when a variants overlaps with multiple CNV regions Issue: 524
genesToBarcodes sample selection fix
coOncoplot bug fix with showSampleNames argument. Issue: 306

OncogenicPathways improvements Issue: #505
Added showSum, colNC, nShiftSymbols, sigSymbolsSize, sigSymbolsFontSize, pvSymbols arguments to somaticInteractions PR: #505 Thanks zmiimz
Added anno_height, drawBox, drawExtraBar arguments to oncoplot PR: #501 Thanks Kai Gu
Added decreasing argument to tcgaComapre Issue: #497
Added startgain and startlost to annovarToMaf Issue: #487
y_lims argument in gisticChromPlot Issue: #485
Added support for highlighting multiple additionalFeatures Issue: #476
Pairwise t-test and mutational load in tcgaCompare Issue: #453
Added titleText argument to oncoplot Issue: #448
Highlight mutated genes on gisticChromplot Issue: #443
Added legend_height argument to oncoplot Issue: #346
Added bgBorderCol domainBorderCol showLegend argument to lollipopPlot

tmb Simple tumor mutation burden estimation function.
setdiffMAF and intersectMAF. Set operations for MAF files. PR: #508 Thanks Shixiang Wang
tcgaDriverBP Compare genes to known TCGA drivers and their biological pathways
vafCompare plots vaf distribution of target genes from two cohorts Issue: #495
coBarplot side-by-side barplot for maf comparison Issue: #486
Group genes in oncoplot by specific pathways. This can be done by setting pathways = 'auto' or by providing a two column data.frame/tsv-file with Gene names and their corresponding pathway belongings.
Oncoplot gains rightBarData and leftBarData arguments for user specific side bar plots.
Default flatUI colors for lollipop plots