Changes in version 3.12 BUG REPORTS - Incorrect deduplication cases while validating MAFs. Issue: 623 - Fix repeated domain labels in lollipopPlot2. Issue: 614 - Fix Copy number labels and coloring in coBarPlot. Issue: 609 - Fix coloring issues for annotations in oncoplot in R < 4.0. Issue: 599 ENHANCEMENTS - Updated TCGA TMB. All variants from MC3 results are restricted and harmonized to Agilent 35.8 MB capture kit. See ?tcgaCompare for details. Issue: 612 - Added SIMC1 protein to domain database. Issue: 616 - Added sampleOrder1 and sampleOrder2 arguments to coOncoplot. Issue: 592 - Added gene_mar outer_mar argument to coOncoplot. Issue: 260 - Added sample size warning messages to mafCompare. Issue: 602 - Added cohortFontSize and axisFontSize to tcgaCompare NEW FUNCTIONS - Added filterMaf function. DEPRECATED - signatureEnrichment will be deprecated in future. Currently kept for legacy purpose with a warning message. Issue: 607 615 Changes in version 2.6.05 BUG REPORTS - mafSurvival Remove non functional fn argument. Issue: 660 - OncogenicPathways zero entries bug and correct documentation. Issue: 656 - plotApobecDiff y-axis limits. Issue: 642 629 - Rainfallplot arrowhead bug. Issue: 628 629 ENHANCEMENTS - Improve clinicalEnrichment odd-ratio interpretation. Issue: 633 In earlier versions, odds-ratio indicated the odds of observing WT in the group of interest compared to Mutant. From this update, odds-ratio indicate the odds of observing mutant in the group of interest compared to wild-type. This way is much intuitive and easier interpret. See issue 633 for details. P-values and other details are unaffected. - Changes in how Multi_Hit are reported. By default two distinct types of mutations in the same gene or same patient were classified as Multi_Hit (e.g; Missense + Splice_Site = Multi_Hit; Missense + Missense = Missense). This update onward, regardless of type of mutations, if there are >1 mutations in the same gene of same patient, they are classified as Multi_Hit (e.g; Missense + Splice_Site = Multi_Hit; Missense + Missense = Multi_Hit). Issue: 347 347