[{"data":1,"prerenderedAt":742},["ShallowReactive",2],{"navigation":3,"/pecan/data-facets/use-cases":421,"/pecan/data-facets/use-cases-surround":739},[4,19,25,131,197],{"title":5,"_path":6,"children":7,"icon":18},"Overview","/overview",[8,9,12,15],{"title":5,"_path":6},{"title":10,"_path":11},"About our Ecosystem","/overview/ecosystem",{"title":13,"_path":14},"Citing St. Jude Cloud","/overview/citing-stjude-cloud",{"title":16,"_path":17},"Frequently Asked Questions","/overview/faq","sjc-icon:child-logo",{"title":20,"_path":21,"children":22,"icon":24},"CC4K","/cc4k",[23],{"title":5,"_path":21},"sjc-icon:ontology-tree",{"title":26,"_path":27,"children":28,"icon":130},"Genomics Platform","/genomics-platform",[29,49,62,80,99],{"title":30,"_path":31,"children":32},"Getting Started","/genomics-platform/getting-started",[33,35,38,41,44,46],{"title":5,"_path":34},"/genomics-platform/getting-started/overview",{"title":36,"_path":37},"Accounts and Billing","/genomics-platform/getting-started/accounts-and-billing",{"title":39,"_path":40},"Making a Data Request","/genomics-platform/getting-started/making-a-data-request",{"title":42,"_path":43},"Filling Out the DAA","/genomics-platform/getting-started/filling-out-the-daa",{"title":16,"_path":45},"/genomics-platform/getting-started/faq",{"title":47,"_path":48},"Glossary","/genomics-platform/getting-started/glossary",{"title":50,"_path":51,"children":52},"About Our Data","/genomics-platform/about-our-data",[53,56,59],{"title":54,"_path":55},"Data Sets and Data Access Units","/genomics-platform/about-our-data/data-sets-and-data-access-units",{"title":57,"_path":58},"File Formats and Sequencing Information","/genomics-platform/about-our-data/file-formats-and-sequencing-information",{"title":60,"_path":61},"Metadata and Clinical Information","/genomics-platform/about-our-data/metadata-and-clinical-information",{"title":63,"_path":64,"children":65},"Managing Data","/genomics-platform/managing-data",[66,68,71,74,77],{"title":5,"_path":67},"/genomics-platform/managing-data/overview",{"title":69,"_path":70},"Upload/Download Data (Local)","/genomics-platform/managing-data/upload-download-data-local",{"title":72,"_path":73},"Upload/Download Data (Cluster)","/genomics-platform/managing-data/upload-download-data-cluster",{"title":75,"_path":76},"Upload/Download Data (DNAnexus)","/genomics-platform/managing-data/upload-download-data-dnanexus",{"title":78,"_path":79},"Renewing Your DAA","/genomics-platform/managing-data/renewing-your-daa",{"title":81,"_path":82,"children":83},"Analyzing Data","/genomics-platform/analyzing-data",[84,87,90,93,96],{"title":85,"_path":86},"Command Line Interaction","/genomics-platform/analyzing-data/command-line-interaction",{"title":88,"_path":89},"Running Our Workflows","/genomics-platform/analyzing-data/running-our-workflows",{"title":91,"_path":92},"Creating a Cloud Application","/genomics-platform/analyzing-data/creating-a-cloud-app",{"title":94,"_path":95},"Interactive Nodes","/genomics-platform/analyzing-data/interactive-nodes",{"title":97,"_path":98},"Visualizing NGS Data","/genomics-platform/analyzing-data/visualizing-ngs-data",{"title":100,"_path":101,"children":102},"Workflow Guides","/genomics-platform/workflow-guides",[103,106,109,112,115,118,121,124,127],{"title":104,"_path":105},"ChIP-Seq Peak Calling","/genomics-platform/workflow-guides/chipseq",{"title":107,"_path":108},"cis-X","/genomics-platform/workflow-guides/cisx",{"title":110,"_path":111},"MethylationToActivity","/genomics-platform/workflow-guides/methylation-to-activity",{"title":113,"_path":114},"Mutational Signatures","/genomics-platform/workflow-guides/mutational-signatures",{"title":116,"_path":117},"Rapid RNA-Seq","/genomics-platform/workflow-guides/rapid-rnaseq",{"title":119,"_path":120},"RNA-Seq Expression Classification","/genomics-platform/workflow-guides/rnaseq-expression-classification",{"title":122,"_path":123},"SEAseq","/genomics-platform/workflow-guides/seaseq",{"title":125,"_path":126},"SequencErr","/genomics-platform/workflow-guides/sequencerr",{"title":128,"_path":129},"WARDEN Differential Gene Expression","/genomics-platform/workflow-guides/warden","sjc-icon:genomics-platform",{"title":132,"_path":133,"children":134,"icon":196},"PeCan","/pecan",[135,149,156,174,181,190],{"title":5,"_path":136,"children":137},"/pecan/overview",[138,140,143,146],{"title":30,"_path":139},"/pecan/overview/getting-started",{"title":141,"_path":142},"Methods and Data","/pecan/overview/methods-and-data",{"title":144,"_path":145},"Videos","/pecan/overview/videos",{"title":147,"_path":148},"FAQ","/pecan/overview/faq",{"title":150,"_path":151,"children":152},"Cohort Building","/pecan/cohort-building",[153],{"title":154,"_path":155},"Create Custom Cohorts","/pecan/cohort-building/cohort-building",{"title":157,"_path":158,"children":159},"Data Facets","/pecan/data-facets",[160,163,165,168,171],{"title":161,"_path":162},"Variants","/pecan/data-facets/variants",{"title":113,"_path":164},"/pecan/data-facets/mutational-signatures",{"title":166,"_path":167},"Expression","/pecan/data-facets/expression",{"title":169,"_path":170},"Histology","/pecan/data-facets/histology",{"title":172,"_path":173},"Use Cases","/pecan/data-facets/use-cases",{"title":175,"_path":176,"children":177},"Accessibility","/pecan/accessibility",[178],{"title":179,"_path":180},"Keyboard Shortcuts","/pecan/accessibility/keyboard-shortcuts",{"title":182,"_path":183,"children":184},"PeCan PIE","/pecan/pecan-pie",[185,188],{"title":186,"_path":187},"What is PIE","/pecan/pecan-pie/what-is-pie",{"title":147,"_path":189},"/pecan/pecan-pie/faq",{"title":191,"_path":192,"children":193},"Release Notes","/pecan/release-notes",[194],{"title":195,"_path":192},"PeCan Release Notes","sjc-icon:pecan",{"title":198,"_path":199,"children":200,"icon":420},"Visualization Community","/visualization-community",[201,215,246,307,411],{"title":5,"_path":202,"children":203},"/visualization-community/overview",[204,207,210,213],{"title":205,"_path":206},"What is Visualization Community","/visualization-community/overview/what-is-visualization-community",{"title":208,"_path":209},"What are ProteinPaint and GenomePaint","/visualization-community/overview/what-are-proteinpaint-and-genome-paint",{"title":211,"_path":212},"Data Types","/visualization-community/overview/data-types-and-graphs",{"title":147,"_path":214},"/visualization-community/overview/faq",{"title":30,"_path":216,"children":217},"/visualization-community/getting-started",[218,220,223,226,229,232,235,238,241,243],{"title":5,"_path":219},"/visualization-community/getting-started/overview",{"title":221,"_path":222},"How to Sign-in","/visualization-community/getting-started/how-to-sign-in",{"title":224,"_path":225},"How to Use the VisEditor","/visualization-community/getting-started/how-to-use-the-viseditor",{"title":227,"_path":228},"Tracks and Apps","/visualization-community/getting-started/tracks-and-apps",{"title":230,"_path":231},"Manage Your Data","/visualization-community/getting-started/manage-your-data",{"title":233,"_path":234},"Collections & Communities","/visualization-community/getting-started/collections-and-communities",{"title":236,"_path":237},"Public vs. Private Visualizations","/visualization-community/getting-started/public-vs-private-visualizations",{"title":239,"_path":240},"Embedding","/visualization-community/getting-started/embedding",{"title":144,"_path":242},"/visualization-community/getting-started/videos",{"title":244,"_path":245},"NEW Data Download","/visualization-community/getting-started/new-data-download",{"title":247,"_path":248,"children":249},"Code Block Library","/visualization-community/code-block-library",[250,253,256,259,262,265,268,271,274,277,280,283,286,289,292,295,298,301,304],{"title":251,"_path":252},"Code Block Basics","/visualization-community/code-block-library/code-block-basics",{"title":254,"_path":255},"Allelic Imbalance","/visualization-community/code-block-library/allelic-imbalance",{"title":257,"_path":258},"Arc","/visualization-community/code-block-library/arc",{"title":260,"_path":261},"BAM","/visualization-community/code-block-library/bam",{"title":263,"_path":264},"BigWig","/visualization-community/code-block-library/bigwig",{"title":266,"_path":267},"BigWig Stranded","/visualization-community/code-block-library/bigwig-stranded",{"title":269,"_path":270},"Expression Rank","/visualization-community/code-block-library/expression-rank",{"title":272,"_path":273},"Hi-C","/visualization-community/code-block-library/hi-c",{"title":275,"_path":276},"Heatmap","/visualization-community/code-block-library/heatmap",{"title":278,"_path":279},"JSON BED","/visualization-community/code-block-library/json-bed",{"title":281,"_path":282},"Lollipop","/visualization-community/code-block-library/lollipop",{"title":284,"_path":285},"MA Volcano","/visualization-community/code-block-library/ma-volcano",{"title":287,"_path":288},"Profile Gene Value","/visualization-community/code-block-library/profile-gene-value",{"title":290,"_path":291},"RNA Splice Junction","/visualization-community/code-block-library/rna-splice-junction",{"title":293,"_path":294},"Single Cell","/visualization-community/code-block-library/single-cell",{"title":296,"_path":297},"Splice Junctions Cohort","/visualization-community/code-block-library/splice-junctions-cohort",{"title":299,"_path":300},"Track List and Facet Table","/visualization-community/code-block-library/track-list-and-facet-table",{"title":302,"_path":303},"t-SNE","/visualization-community/code-block-library/t-sne",{"title":305,"_path":306},"VCF","/visualization-community/code-block-library/vcf",{"title":308,"_path":309,"children":310},"ProteinPaint","/visualization-community/proteinpaint",[311,313,316,318,321,324,327,330,333,336,339,342,345,348,351,354,357,360,363,366,369,372,375,378,381,384,387,390,393,396,399,402,405,408],{"title":308,"_path":312},"/visualization-community/proteinpaint/proteinpaint",{"title":314,"_path":315},"Introduction","/visualization-community/proteinpaint/introduction",{"title":30,"_path":317},"/visualization-community/proteinpaint/getting-started",{"title":319,"_path":320},"Loading Datasets","/visualization-community/proteinpaint/loading-datasets",{"title":322,"_path":323},"Viewing SNV/Indel Mutations","/visualization-community/proteinpaint/viewing-snv-indel-mutations",{"title":325,"_path":326},"Viewing Gene Fusions","/visualization-community/proteinpaint/viewing-gene-fusions",{"title":328,"_path":329},"Viewing Expression Data","/visualization-community/proteinpaint/viewing-expression-data",{"title":331,"_path":332},"Filtering Mutations","/visualization-community/proteinpaint/filtering-mutations",{"title":334,"_path":335},"Exporting Figures and Data","/visualization-community/proteinpaint/exporting-figures-and-data",{"title":337,"_path":338},"Using the Gene Table","/visualization-community/proteinpaint/using-the-gene-table",{"title":340,"_path":341},"Using the Sample Table","/visualization-community/proteinpaint/using-the-sample-table",{"title":343,"_path":344},"Using the Heatmap","/visualization-community/proteinpaint/using-the-heatmap",{"title":346,"_path":347},"Using Disease Pie Charts","/visualization-community/proteinpaint/using-disease-pie-charts",{"title":349,"_path":350},"Stratifying Mutations by Cancer Subtype","/visualization-community/proteinpaint/stratifying-mutations-by-cancer-subtype",{"title":352,"_path":353},"SNV and Indel","/visualization-community/proteinpaint/snv-and-indel",{"title":355,"_path":356},"SV and fusion transcript","/visualization-community/proteinpaint/sv-and-fusion-transcript",{"title":358,"_path":359},"Copy Number Variants","/visualization-community/proteinpaint/copy-number-variants",{"title":361,"_path":362},"Internal tandem duplications","/visualization-community/proteinpaint/internal-tandem-duplications",{"title":364,"_path":365},"Intragenic deletion","/visualization-community/proteinpaint/intragenic-deletion",{"title":367,"_path":368},"Truncation, N-loss, or C-loss","/visualization-community/proteinpaint/truncation",{"title":370,"_path":371},"JSON-BED","/visualization-community/proteinpaint/json-bed",{"title":373,"_path":374},"Splice Junction","/visualization-community/proteinpaint/splice-junction",{"title":376,"_path":377},"Profile-Gene-Value","/visualization-community/proteinpaint/profile-gene-value",{"title":379,"_path":380},"Bampile","/visualization-community/proteinpaint/bampile",{"title":382,"_path":383},"Add Custom Protein Domains","/visualization-community/proteinpaint/add-custom-protein-domains",{"title":385,"_path":386},"Using Custom Tracks","/visualization-community/proteinpaint/using-custom-tracks",{"title":388,"_path":389},"Visualize Your Mutation Data","/visualization-community/proteinpaint/visualize-your-mutation-data",{"title":391,"_path":392},"Loading SNV/Indel Mutations from a File","/visualization-community/proteinpaint/loading-mutations-from-file",{"title":394,"_path":395},"Uploaded Mutation Data User Interface","/visualization-community/proteinpaint/uploaded-mutation-data",{"title":397,"_path":398},"Loading a TCGA MAF File","/visualization-community/proteinpaint/loading-tcga-maf-file",{"title":400,"_path":401},"Using a VCF File","/visualization-community/proteinpaint/using-vcf-file",{"title":403,"_path":404},"Embedding ProteinPaint","/visualization-community/proteinpaint/embedding-proteinpaint",{"title":406,"_path":407},"URL Parameters","/visualization-community/proteinpaint/url-parameters",{"title":409,"_path":410},"Organizing Data into a Study View","/visualization-community/proteinpaint/study-view",{"title":412,"_path":413,"children":414},"GenomePaint","/visualization-community/genomepaint",[415,417],{"title":412,"_path":416},"/visualization-community/genomepaint/genomepaint",{"title":418,"_path":419},"GenomePaint User Guide","/visualization-community/genomepaint/genomepaint-user-guide","sjc-icon:viz",{"_path":173,"_dir":422,"_draft":423,"_partial":423,"_locale":424,"title":425,"description":426,"navigation":427,"body":428,"_type":733,"_id":734,"_source":735,"_file":736,"_stem":737,"_extension":738},"data-facets",false,"","Common Use Cases","The following are common scenarios a user might want to achieve in PeCan.",{"title":172},{"type":429,"children":430,"toc":730},"root",[431,438,718],{"type":432,"tag":433,"props":434,"children":435},"element","p",{},[436],{"type":437,"value":426},"text",{"type":432,"tag":439,"props":440,"children":441},"ol",{},[442,473,509,534,563,574,594,610,633,658,673,688,703],{"type":432,"tag":443,"props":444,"children":445},"li",{},[446,448,457,459,464,466,471],{"type":437,"value":447},"The ",{"type":432,"tag":449,"props":450,"children":454},"a",{"href":451,"rel":452},"https://pecan.stjude.cloud/",[453],"nofollow",[455],{"type":437,"value":456},"homepage",{"type":437,"value":458}," is designed to familiarize the user with the components of the platform along with key features found in each.\nAdditionally, the user can explore our ",{"type":432,"tag":449,"props":460,"children":461},{"href":139},[462],{"type":437,"value":463},"Help Guides",{"type":437,"value":465}," which allows the user to read more about each data facet, including the ",{"type":432,"tag":449,"props":467,"children":468},{"href":142},[469],{"type":437,"value":470},"data and methods",{"type":437,"value":472}," to generate each facet.",{"type":432,"tag":443,"props":474,"children":475},{},[476,478,485,487,494,496],{"type":437,"value":477},"A user can navigate to ",{"type":432,"tag":449,"props":479,"children":482},{"href":480,"rel":481},"https://pecan.stjude.cloud/pie",[453],[483],{"type":437,"value":484},"PIE",{"type":437,"value":486}," and once signed in, the user can ",{"type":432,"tag":449,"props":488,"children":491},{"href":489,"rel":490},"https://pecan.stjude.cloud/pie/submit-job",[453],[492],{"type":437,"value":493},"submit a job",{"type":437,"value":495}," which allows the upload of a VCF file or the ability to enter a single variant.\n",{"type":432,"tag":497,"props":498,"children":499},"strong",{},[500,502,507],{"type":437,"value":501},"Read more information about PIE ",{"type":432,"tag":449,"props":503,"children":504},{"href":187},[505],{"type":437,"value":506},"here",{"type":437,"value":508},".",{"type":432,"tag":443,"props":510,"children":511},{},[512,514,521,523],{"type":437,"value":513},"On the ",{"type":432,"tag":449,"props":515,"children":518},{"href":516,"rel":517},"https://pecan.stjude.cloud/histology",[453],[519],{"type":437,"value":520},"histology",{"type":437,"value":522}," data facet, a user can search on the advanced search page so a specific CompBioID.\nThis does not populate approximates but a user can search partial IDs.\n",{"type":432,"tag":497,"props":524,"children":525},{},[526,528,533],{"type":437,"value":527},"Read more about ",{"type":432,"tag":449,"props":529,"children":530},{"href":170},[531],{"type":437,"value":532},"Histology here",{"type":437,"value":508},{"type":432,"tag":443,"props":535,"children":536},{},[537,538,543,545,552,554],{"type":437,"value":513},{"type":432,"tag":449,"props":539,"children":541},{"href":516,"rel":540},[453],[542],{"type":437,"value":520},{"type":437,"value":544}," data facet, a user can select a histology image and then navigate to the ",{"type":432,"tag":546,"props":547,"children":549},"code",{"className":548},[],[550],{"type":437,"value":551},"Open Viewer",{"type":437,"value":553}," whereby the user can expect the histology image using the OpenSeaDragon features.\n",{"type":432,"tag":497,"props":555,"children":556},{},[557,558,562],{"type":437,"value":527},{"type":432,"tag":449,"props":559,"children":560},{"href":170},[561],{"type":437,"value":532},{"type":437,"value":508},{"type":432,"tag":443,"props":564,"children":565},{},[566,567,572],{"type":437,"value":513},{"type":432,"tag":449,"props":568,"children":570},{"href":516,"rel":569},[453],[571],{"type":437,"value":520},{"type":437,"value":573}," data facet, a user can select a histology image and then access the relevant clinical notes per slide.",{"type":432,"tag":443,"props":575,"children":576},{},[577,578,583,585],{"type":437,"value":513},{"type":432,"tag":449,"props":579,"children":581},{"href":516,"rel":580},[453],[582],{"type":437,"value":520},{"type":437,"value":584}," data facet, a user can select a histology image and copy the URL to share with others and/or download the image for personal use.\nThese two features can also be accessed on the Open Viewer page.\n",{"type":432,"tag":497,"props":586,"children":587},{},[588,589,593],{"type":437,"value":527},{"type":432,"tag":449,"props":590,"children":591},{"href":170},[592],{"type":437,"value":532},{"type":437,"value":508},{"type":432,"tag":443,"props":595,"children":596},{},[597,599],{"type":437,"value":598},"On the Sunburst, the user can select a disease and/or subtype which then updates the patient and sample stat summary in the top left.\nAvailable samples will also update accordingly per data facet.\n",{"type":432,"tag":497,"props":600,"children":601},{},[602,604,609],{"type":437,"value":603},"Read more on ",{"type":432,"tag":449,"props":605,"children":606},{"href":139},[607],{"type":437,"value":608},"Getting Started here",{"type":437,"value":508},{"type":432,"tag":443,"props":611,"children":612},{},[613,615,621,623],{"type":437,"value":614},"The user can search a gene which takes them to the ProteinPaint view in the Variants data facet.\nHere, no filtering will be precomputed and the ",{"type":432,"tag":546,"props":616,"children":618},{"className":617},[],[619],{"type":437,"value":620},"Pedatric",{"type":437,"value":622}," dataset for hg38 will be defaulted.\nThe user can navigate to the Variants data facet and click on ProteinPaint.\nThe default view will be for TP53 with hg38 genome.\nThe user can filter by diagnosis and/or subtype or move coordinates by typing a new gene in the width container.\n",{"type":432,"tag":497,"props":624,"children":625},{},[626,627,632],{"type":437,"value":527},{"type":432,"tag":449,"props":628,"children":629},{"href":162},[630],{"type":437,"value":631},"Variants:ProteinPaint here",{"type":437,"value":508},{"type":432,"tag":443,"props":634,"children":635},{},[636,638],{"type":437,"value":637},"The user can search a variant which takes them to the Variant Details page in the Variants data facet.\nHere, the variant information will be defaulted to hg19.\nThe user can navigate to the Variants data facet and click on ProteinPaint.\nThe default view will be for TP53 with hg38 genome.\nThe user can filter by diagnosis and/or subtype or move coordinates by typing a new gene in the width container.\nThe user can find a Variant Details page two ways:\n",{"type":432,"tag":639,"props":640,"children":641},"ul",{},[642,647],{"type":432,"tag":443,"props":643,"children":644},{},[645],{"type":437,"value":646},"Hover underneath all variants which will display a total number.\nBy clicking the total it will populate a table where a Variant Details blue box will appear.\nThis is clickable which will populate all P/LP buttons.\nSelect one to view the variant page.",{"type":432,"tag":443,"props":648,"children":649},{},[650,652,657],{"type":437,"value":651},"Click a variant of interest on the lollipop and click the P/LP button to view the variant page.\nRead more about ",{"type":432,"tag":449,"props":653,"children":654},{"href":162},[655],{"type":437,"value":656},"Variants:Variant Details here",{"type":437,"value":508},{"type":432,"tag":443,"props":659,"children":660},{},[661,663],{"type":437,"value":662},"A user can filter on the subtype search and then select the Variants data facet which will render the appropriate oncoprint.\nA user can navigate to the Variants data facet without filtering from the subtype search and then use the Variants dropdown filter accordingly.\n",{"type":432,"tag":497,"props":664,"children":665},{},[666,667,672],{"type":437,"value":527},{"type":432,"tag":449,"props":668,"children":669},{"href":162},[670],{"type":437,"value":671},"Variants:Oncoprint here",{"type":437,"value":508},{"type":432,"tag":443,"props":674,"children":675},{},[676,678],{"type":437,"value":677},"A user can filter on the subtype search and then select the Variants data facet and toggle to Variant Prevalence which will render the appropriate visualization.\nA user can navigate to the Variants data facet without filtering from the subtype search and then use the Variants dropdown filter accordingly.\n",{"type":432,"tag":497,"props":679,"children":680},{},[681,682,687],{"type":437,"value":527},{"type":432,"tag":449,"props":683,"children":684},{"href":162},[685],{"type":437,"value":686},"Variants:Variant Prevalence here",{"type":437,"value":508},{"type":432,"tag":443,"props":689,"children":690},{},[691,693],{"type":437,"value":692},"A user can prefilter by the subtype search, subtype tree or navigate directly into the data facet.\nHere, a user can select samples by subtype (y-axis), mutational signature (x-axis), or subtype with a specific mutational signature (cell).\nThe selection will populate a sample summary page.\n",{"type":432,"tag":497,"props":694,"children":695},{},[696,697,702],{"type":437,"value":527},{"type":432,"tag":449,"props":698,"children":699},{"href":164},[700],{"type":437,"value":701},"Mutational Signatures here",{"type":437,"value":508},{"type":432,"tag":443,"props":704,"children":705},{},[706,708],{"type":437,"value":707},"A user can employ the lasso feature where you draw a region on the map and then select \"list samples\".\n",{"type":432,"tag":497,"props":709,"children":710},{},[711,712,717],{"type":437,"value":527},{"type":432,"tag":449,"props":713,"children":714},{"href":167},[715],{"type":437,"value":716},"Expression here",{"type":437,"value":508},{"type":432,"tag":433,"props":719,"children":720},{},[721,723,729],{"type":437,"value":722},"Interested in a new feature?\nSubmit your idea to ",{"type":432,"tag":449,"props":724,"children":726},{"href":725},"mailto:support@stjude.cloud",[727],{"type":437,"value":728},"support@stjude.cloud",{"type":437,"value":508},{"title":424,"searchDepth":731,"depth":731,"links":732},2,[],"markdown","content:4.pecan:3.data-facets:5.use-cases.md","content","4.pecan/3.data-facets/5.use-cases.md","4.pecan/3.data-facets/5.use-cases","md",[740,741],{"_path":170,"title":169,"description":424},{"_path":180,"title":179,"description":424},1791243639355]