maftools: Summarize, Analyze and Visualize MAF files

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

AuthorAnand Mayakonda <anand_mt@hotmail.com>
Date of publicationNone
MaintainerAnand Mayakonda <anand_mt@hotmail.com>
LicenseMIT + file LICENSE
Version1.0.40
https://github.com/PoisonAlien/maftools

View on Bioconductor

Man pages

annovarToMaf: Converts annovar annotations into MAF.

coOncoplot: Draw two oncoplots side by side for cohort comparision.

extractSignatures: Extract mutational signatures from trinucletide context.

forestPlot: Draw forest plot for differences betweeen cohorts.

geneCloud: Plots wordcloud.

genesToBarcodes: Extracts Tumor Sample Barcodes where the given genes are...

getCytobandSummary: extract cytoband summary from GISTIC object

getFields: extract available fields from MAF object

getGeneSummary: extract gene summary from MAF or GISTIC object

getSampleSummary: extract sample summary from MAF or GISTIC object

GISTIC-class: Class GISTIC

gisticPlot: Plot gistic results.

icgcSimpleMutationToMAF: Converts ICGC Simple Somatic Mutation format file to MAF

inferHeterogeneity: Clusters variants based on Variant Allele Frequencies (VAF).

lollipopPlot: Draws lollipop plot of amino acid changes on to Protein...

MAF-class: Class MAF

mafCompare: compare two cohorts (MAF).

math.score: calculates MATH (Mutant-Allele Tumor Heterogeneity) score.

mutExclusive: Performs exact test for mutual exclusive events.

oncodrive: Detect cancer driver genes based on positional clustering of...

oncoplot: draw an oncoplot

oncostrip: draw an oncostrip similar to cBioportal oncoprinter output.

oncotate: Annotates given variants using oncotator api.

pfamDomains: pfam domain annotation and summarization.

plotCBSsegments: Plots segmented copy number data.

plotClusters: Plot density plots from clutering results.

plotGisticResults: Plot gistic results as a bubble plot.

plotmafSummary: Plots maf summary.

plotOncodrive: Plots results from 'oncodrive'

plotSignatures: Plots decomposed mutational signatures.

plotTiTv: Plot Transition and Trasnversion ratios.

plotVaf: Plots vaf distribution of genes

rainfallPlot: Rainfall plot to display kataegis or hyper mutated genomic...

readGistic: Read and summarize gistic output.

read.maf: Read MAF files.

subsetMaf: Subset MAF

titv: Classifies SNPs into transitions and transversions

trinucleotideMatrix: Extract single 5' and 3' bases flanking the mutated site.

vcr: Samll internal function to make complex events.

write.GisticSummary: Writes GISTIC summaries to output tab-delimited text files.

write.mafSummary: Writes maf summaries to output tab-delimited text files.

Files in this package

maftools/DESCRIPTION
maftools/LICENSE
maftools/NAMESPACE
maftools/R
maftools/R/TrinucleotideMatrix.R maftools/R/addOncoprint.R maftools/R/annovarToMaf.R maftools/R/clusterScore.R maftools/R/coOncoplot.R maftools/R/dashboard.R maftools/R/domainSummary.R maftools/R/extractSignatures.R maftools/R/filterCopyNumber.R maftools/R/fisherCorrect.R maftools/R/forestPlot.R maftools/R/geneCloud.R maftools/R/genesToBarcodes.R maftools/R/getOncoPlot.R maftools/R/gisticObject.R maftools/R/gisticPlot.R maftools/R/icgc_to_maf.R maftools/R/inferTumHetero.R maftools/R/lollipopPlot.R maftools/R/mafCompare.R maftools/R/mafObjects.R maftools/R/maf_methods.R maftools/R/mathScore.R maftools/R/mutExclusive.R maftools/R/oncodrive.R maftools/R/oncoplot.R maftools/R/oncostrip.R maftools/R/oncotate.R maftools/R/plotClusters.R maftools/R/plotGisticResults.R maftools/R/plotMafSummary.R maftools/R/plotOncodriveClust.R maftools/R/plotSignatures.R maftools/R/plotTiTv.R maftools/R/plot_cbs_segs.R maftools/R/plot_vaf.R maftools/R/rainfallPlot.R maftools/R/readGistic.R maftools/R/readSegs.R maftools/R/read_maf_dt.R maftools/R/refineClusters.R maftools/R/repelPoints.R maftools/R/subsetMaf.R maftools/R/summarizeGistic.R maftools/R/summarizeMaf.R maftools/R/titv.R maftools/R/validateMaf.R maftools/R/vcr.R maftools/R/writeGisticSummary.R maftools/R/wrteMafSummary.R
maftools/README.md
maftools/build
maftools/build/vignette.rds
maftools/inst
maftools/inst/CITATION
maftools/inst/NEWS
maftools/inst/doc
maftools/inst/doc/maftools.R
maftools/inst/doc/maftools.Rmd
maftools/inst/doc/maftools.html
maftools/inst/extdata
maftools/inst/extdata/APL_primary.maf.gz
maftools/inst/extdata/APL_relapse.maf.gz
maftools/inst/extdata/TCGA.AB.3009.hg19.seg.txt
maftools/inst/extdata/all_lesions.conf_99.txt
maftools/inst/extdata/amp_genes.conf_99.txt
maftools/inst/extdata/coad.maf.gz
maftools/inst/extdata/del_genes.conf_99.txt
maftools/inst/extdata/ensGenes.txt.gz
maftools/inst/extdata/prot_len.txt.gz
maftools/inst/extdata/protein_domains.txt.gz
maftools/inst/extdata/signatures.txt
maftools/inst/extdata/simple_somatic_mutation.open.ESCA-CN.sample.tsv.gz
maftools/inst/extdata/tcga_laml.maf.gz
maftools/inst/extdata/tcga_laml_fab_annotation.txt
maftools/inst/extdata/variants.hg19_multianno.txt
maftools/inst/extdata/variants.tsv
maftools/man
maftools/man/GISTIC-class.Rd maftools/man/MAF-class.Rd maftools/man/annovarToMaf.Rd maftools/man/coOncoplot.Rd maftools/man/extractSignatures.Rd maftools/man/forestPlot.Rd maftools/man/geneCloud.Rd maftools/man/genesToBarcodes.Rd maftools/man/getCytobandSummary.Rd maftools/man/getFields.Rd maftools/man/getGeneSummary.Rd maftools/man/getSampleSummary.Rd maftools/man/gisticPlot.Rd maftools/man/icgcSimpleMutationToMAF.Rd maftools/man/inferHeterogeneity.Rd maftools/man/lollipopPlot.Rd maftools/man/mafCompare.Rd maftools/man/math.score.Rd maftools/man/mutExclusive.Rd maftools/man/oncodrive.Rd maftools/man/oncoplot.Rd maftools/man/oncostrip.Rd maftools/man/oncotate.Rd maftools/man/pfamDomains.Rd maftools/man/plotCBSsegments.Rd maftools/man/plotClusters.Rd maftools/man/plotGisticResults.Rd maftools/man/plotOncodrive.Rd maftools/man/plotSignatures.Rd maftools/man/plotTiTv.Rd maftools/man/plotVaf.Rd maftools/man/plotmafSummary.Rd maftools/man/rainfallPlot.Rd maftools/man/read.maf.Rd maftools/man/readGistic.Rd maftools/man/subsetMaf.Rd maftools/man/titv.Rd maftools/man/trinucleotideMatrix.Rd maftools/man/vcr.Rd maftools/man/write.GisticSummary.Rd maftools/man/write.mafSummary.Rd
maftools/vignettes
maftools/vignettes/maftools.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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