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| GenVisR-package | GenVisR |
| brcaMAF | Truncated BRCA MAF file |
| cnFreq | Construct copy-number frequency plot |
| cnFreq_buildMain | Construct CN frequency plot |
| cnFreq_qual | check input to cnFreq |
| cnSpec | Construct copy-number cohort plot |
| cnSpec_buildMain | Construct CN cohort plot |
| cnSpec_qual | Construct CN cohort plot |
| cnView | Construct copy-number single sample plot |
| cnView_buildMain | construct CN plot |
| cnView_qual | check input to cnView |
| compIdent | Construct identity snp comparison plot |
| compIdent_bamRcnt | Count nucleotide reads at SNP locations |
| compIdent_bamRcnt_qual | Count nucleotide reads at SNP locations |
| compIdent_buildMain | Compare sample identities |
| compIdent_format | Format readcount tables from compIdent |
| covBars | Construct an overall coverage cohort plot |
| covBars_buildMain | Construct coverage cohort plot |
| covBars_qual | Construct coverage cohort plot |
| cytoGeno | Cytogenetic banding dataset |
| genCov | Construct a region of interest coverage plot |
| genCov_alignPlot | align plots on an axis |
| genCov_assign_ggplotGrob_height | assign ggplotGrob height |
| genCov_assign_ggplotGrob_width | assign ggplotGrob width |
| genCov_buildCov | build coverage plot |
| genCov_buildTrack | build label for plot |
| genCov_extr_ggplotGrob_height | extract ggplotGrob height |
| genCov_extr_ggplotGrob_width | extract ggplotGrob width |
| genCov_qual | Perform quality control on genCov data |
| genCov_trackViz | Overlay tracks with plots |
| geneViz | Construct a gene-features plot |
| geneViz_buildGene | build gene plot |
| geneViz_calcGC | Calculate GC content |
| geneViz_cdsFromTXID | cdsFromTXID |
| geneViz_extrCDS | Extract CDS |
| geneViz_extrUTR | Extract UTR |
| geneViz_formatCDS | format cds |
| geneViz_formatUTR | format UTR |
| geneViz_Granges2dataframe | Convert Granges object to dataframe |
| geneViz_mapCoordSpace | Map regions to transformed space |
| geneViz_mapCovCoordSpace | Map coverage track regions to transformed space |
| geneViz_mergeRegions | Create Region Table |
| geneViz_mergeTypeRegions | Create Typed Region Table |
| geneViz_mergeTypes | Merge Typed Region Tables |
| GenVisR | GenVisR |
| HCC1395_Germline | Germline Calls |
| HCC1395_N | Normal BAM |
| HCC1395_T | Tumor BAM |
| hg19chr | hg19 chromosome boundaries |
| ideoView | Construct an ideogram |
| ideoView_buildMain | build chromosome |
| ideoView_formatCytobands | reformat cytogenetic band data frame |
| ideoView_qual | Check input to ideoView |
| lohSpec | Plot LOH data |
| lohSpec_buildMain | Plot LOH data |
| lohSpec_fileGlob | Grab data for lohSpec |
| lohSpec_lohCalc | Calculate loh difference |
| lohSpec_qual | Check input to lohSpec |
| lohSpec_slidingWindow | Obtain LOH data |
| lohSpec_stepCalc | Obtain average loh within each step |
| lohSpec_tileCalc | Calculate loh difference |
| lohSpec_tilePosition | Obtain window information |
| lohSpec_tileWindow | Obtain LOH data |
| lohSpec_windowPosition | Obtain window information |
| lohView | Construct LOH chromosome plot |
| lohView_buildMain | construct loh plot |
| lohView_qual | check input to lohView |
| lolliplot | Construct a lolliplot |
| lolliplot_AA2sidechain | Convert AA to side chain classification |
| lolliplot_buildMain | Construct Lolliplot |
| lolliplot_Codon2AA | Convert Codon to AA |
| lolliplot_constructGene | Construct gene information |
| lolliplot_DNAconv | Convert DNA character string |
| lolliplot_dodgeCoordX | dodge coordinates |
| lolliplot_dodgeCoordY | dodge coordinates |
| lolliplot_fetchDomain | fetch protein domains |
| lolliplot_mutationObs | format mutation observations |
| lolliplot_qual | Check input to lolliplot |
| lolliplot_reduceLolli | Reduce Lolli |
| lolliplot_transcriptID2codingSeq | fetch protein length |
| LucCNseg | Truncated CN segments |
| multi_align | align CN/LOH plots on x axis |
| multi_buildClin | plot clinical information |
| multi_chrBound | retrieve and format CN_cohort plot supplemental data |
| multi_cytobandRet | Retrieve cytogenetic bands |
| multi_selectOut | Choose output |
| multi_subsetChr | subset based on chr |
| SNPloci | Identity snps |
| TvTi | Construct transition-transversion plot |
| TvTi_alignPlot | align TvTi plots on y axis |
| TvTi_annoTransTranv | Annotate Transitions and Transversions |
| TvTi_buildMain | build transitions/transversions |
| TvTi_calcTransTranvFreq | Calculate Transition/Transversion Frequency |
| TvTi_convMAF | Convert .maf format to internal format |
| TvTi_convMaf | Convert .maf format to internal format |
| TvTi_qual | Check input to TvTi |
| TvTi_rmIndel | Remove indels |
| TvTi_rmMnuc | Remove multinucleotide codes |
| waterfall | Construct a waterfall plot |
| waterfall_align | align plots |
| waterfall_buildGenePrevelance | plot mutation recurrence in genes |
| waterfall_buildMain | Plot a mutation heatmap |
| waterfall_buildMutBurden_A | plot mutation burden |
| waterfall_buildMutBurden_B | plot mutation burden |
| waterfall_build_proportions | Build mutational profile plot |
| waterfall_calcMutFreq | Calculate Synonymous/Nonsynonymous mutation frequency |
| waterfall_Custom2anno | Convert Custom File |
| waterfall_geneAlt | mutation sample cutoff gene based |
| waterfall_geneRecurCutoff | Mutation Recurrence Cutoff |
| waterfall_geneSort | sort waterfall file by gene |
| waterfall_hierarchyTRV | Hiearchical removal of MAF entries |
| waterfall_MAF2anno | Convert MAF File |
| waterfall_MGI2anno | Convert MGI File |
| waterfall_NA2gene | Assign NA samples a gene |
| waterfall_palette_names | waterfall_palette_names |
| waterfall_qual | Check input to mutSpec |
| waterfall_rmvSilent | Silent Mutation Removal |
| waterfall_sampAlt | mutation sample subset sample based |
| waterfall_sampSort | sort samples in an internal waterfall file. |
| waterfall_select_palette | Helper function to select a colour palette |