{
    "componentChunkName": "component---src-templates-atlas-page-tsx",
    "path": "/nygc/multimodal-pbmc/",
    "result": {"data":{"config":{"frontmatter":{"title":"Data Visualization"}},"page":{"html":"","frontmatter":{"title":"Integrated analysis of multimodal single-cell data","description":"Integrated analysis of multimodal single-cell data","keywords":"Fred Hutch Data Visualization","background":"/img/bg-hex.jpg","icon":null,"footer":"{ \"twitter\": \"https://twitter.com/FHDataViz\", \"linkedIn\": \"https://www.linkedin.com/company/fhdataviz\", \"instagram\": \"https://www.instagram.com/fhdataviz/\" }","models":[{"name":"genes","type":"csv","url":"https://atlas.fredhutch.org/data/nygc/multimodal/rna/summary/gene_map/values.csv"},{"name":"cells","type":"csv","url":"https://atlas.fredhutch.org/data/nygc/multimodal/cells.csv"},{"name":"proteins","type":"csv","url":"https://atlas.fredhutch.org/data/nygc/multimodal/adt/features/gene/values.csv"},{"name":"featuresColor","type":"json","url":"https://atlas.fredhutch.org/data/nygc/multimodal/metadata.json"},{"name":"deGene","type":"csv","url":"https://atlas.fredhutch.org/data/nygc/multimodal/celltype_rna.csv"},{"name":"deProtein","type":"csv","url":"https://atlas.fredhutch.org/data/nygc/multimodal/celltype_protein.csv"}],"transforms":[{"outputs":"[\"cells\"]","steps":"[ {\"name\": \"cells\", \"fn\": \"flatten\", \"data\": \"cells\" } ]"},{"outputs":"[\"genes\"]","steps":"[ {\"name\": \"genes\", \"fn\": \"flatten\", \"data\": \"genes\" } ]"},{"outputs":"[\"proteins\"]","steps":"[ {\"name\": \"proteins\", \"fn\": \"flatten\", \"data\": \"proteins\" } ]"}],"components":[{"component":"atlas-header","props":"{ \"logoPrimary\": \"/img/nygc.svg\", \"logoPrimaryLink\": \"/nygc/multimodal-pbmc\", \"logoHeight\": 100 }"},{"component":"atlas-search","props":"{ \"title\": \"Search Dataset\", \"cell\": \"cells\", \"protein\": \"proteins\", \"logo\": \"/img/nygc-small.svg\", \"showProteinButton\": true, \"showCellButton\": true, \"showGeneButton\": true, \"linkCell\": \"/nygc/multimodal-pbmc/cell/{cell}\", \"linkGene\": \"/nygc/multimodal-pbmc/gene/{gene}\", \"linkProtein\": \"/nygc/multimodal-pbmc/protein/{protein}\" }"},{"component":"atlas-links","props":"{ \"title\": \"Integrated analysis of multimodal single-cell data\", \"text\": \"The simultaneous measurement of multiple modalities, known as multimodal analysis, represents an exciting frontier for single-cell genomics and necessitates new computational methods that can define cellular states based on multiple data types. Here, we introduce ‘weighted-nearest neighbor analysis”, an unsupervised framework to learn the information content of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of hundreds of thousands of human white blood cells alongside a panel of 228 surface proteins, constructing a multimodal reference atlas of the circulating immune system, which you can explore here.\\nFor more information, you can explore our preprint, Seurat v4 software release,\\b and Azimuth - a web app for mapping your datasets to this reference.\", \"links\": [ { \"name\": \"Paper Preprint\", \"url\": \"https://satijalab.org/v4preprint\" }, { \"name\": \"Seurat v4\", \"url\": \"https://satijalab.org/seurat\" },{ \"name\": \"Azimuth\", \"url\": \"https://satijalab.org/azimuth/\" } ] }"},{"component":"atlas-scatter-2d","props":"{ \"title\": \"UMAP\", \"default\": { \"projection\": 0, \"color\": \"observations/featuresColor/2\", \"label\": \"observations/featuresColor/2\", \"dimensions\": 2 }, \"colors\": [ { \"type\": \"observations\", \"options\": \"featuresColor\", \"data\": \"https://atlas.fredhutch.org/data/nygc/multimodal/values.bin\", \"dataType\": \"UI8\" } ], \"projections\": [ { \"title\": \"joint\", \"label\": \"https://atlas.fredhutch.org/data/nygc/multimodal/celltype_joint.json\", \"coords\": \"https://atlas.fredhutch.org/data/nygc/multimodal/adt/projections/jumap/2/values.2d.scaled.bin\", \"camera\": { \"zoom\": -6.7, \"target\": [-8526, -213, 8.003553375601768e-11] } }, { \"title\":\"protein\", \"label\": \"https://atlas.fredhutch.org/data/nygc/multimodal/celltype_protein.json\", \"coords\": \"https://atlas.fredhutch.org/data/nygc/multimodal/adt/projections/aumap/2/values.2d.scaled.bin\", \"camera\": { \"zoom\": -6.7, \"target\": [-8526, -213, 8.003553375601768e-11] } }, { \"title\":\"rna\", \"label\": \"https://atlas.fredhutch.org/data/nygc/multimodal/celltype_rna.json\", \"coords\": \"https://atlas.fredhutch.org/data/nygc/multimodal/adt/projections/umap/2/values.2d.scaled.bin\", \"camera\": { \"zoom\": -6.7, \"target\": [-8526, -213, 8.003553375601768e-11] } } ] }"},{"component":"atlas-table","props":"{  \"title\": \"Differential expression by celltype\", \"csv\": \"deGene\", \"columns\": [ {\"name\":\"Cell Type\",  \"idx\": 1, \"link\": \"cell\"}, {\"name\":\"Gene\", \"idx\": 0, \"link\": \"gene\"}, {\"name\":\"Average Log Fold Change\",  \"idx\": 2, \"fmt\":\".5\", \"sort\": \"desc\"}, {\"name\":\"P Value\",  \"idx\": 3, \"fmt\":\".5\"}\n], \"linkCell\": \"/nygc/multimodal-pbmc/cell/{cell}\", \"linkGene\": \"/nygc/multimodal-pbmc/gene/{gene}\", \"linkProtein\": \"/nygc/multimodal-pbmc/protein/{protein}\" }"},{"component":"atlas-table","props":"{  \"title\": \"Differential abundance by celltype\", \"csv\": \"deProtein\", \"columns\": [ {\"name\":\"Cell Type\",  \"idx\": 1, \"link\": \"cell\"}, {\"name\":\"Protein\", \"idx\": 0, \"link\": \"protein\"}, {\"name\":\"Average Log Fold Change\",  \"idx\": 2, \"fmt\":\".5\", \"sort\": \"desc\"}, {\"name\":\"P Value\",  \"idx\": 3, \"fmt\":\".5\"} ], \"linkCell\": \"/nygc/multimodal-pbmc/cell/{cell}\", \"linkGene\": \"/nygc/multimodal-pbmc/gene/{gene}\", \"linkProtein\": \"/nygc/multimodal-pbmc/protein/{protein}\" }"},{"component":"atlas-downloads","props":"{ \"title\": \"Downloads\", \"sections\":[ { \"headline\":\"\", \"desc\":\"Click below to download a H5 Seruat data file and antibody information\", \"columns\":[], \"files\":[ { \"name\":\"multi.h5seurat\", \"desc\":\"H5 Seurat Data\", \"url\":\"https://atlas.fredhutch.org/data/nygc/multimodal/pbmc_multimodal.h5seurat\", \"size\":\"2.1G\", \"type\":\"H5S\", \"date\":\"2019-12-01\" }, { \"name\":\"Antibody Info\", \"desc\":\"Antibody Info\", \"url\":\"https://atlas.fredhutch.org/data/nygc/multimodal-pbmc/antibodyinfo.csv\", \"size\":\"19K\", \"type\":\"CSV\", \"date\":\"2019-12-01\" } ] } ] }"}]}}},"pageContext":{"id":"944ff178-4026-5b70-9c22-e0eaa476adbf","cid":"436359cb-2391-57ee-8d31-d691fb5401b9"}},
    "staticQueryHashes": []}