{"id":477,"date":"2021-12-02T23:16:18","date_gmt":"2021-12-02T23:16:18","guid":{"rendered":"https:\/\/terrabioappdev.wpenginepowered.com\/discover-how-to-use-human-cell-atlas-data-in-terra\/"},"modified":"2023-12-27T04:55:09","modified_gmt":"2023-12-27T04:55:09","slug":"discover-how-to-use-human-cell-atlas-data-in-terra","status":"publish","type":"post","link":"https:\/\/terra.bio\/discover-how-to-use-human-cell-atlas-data-in-terra\/","title":{"rendered":"Discover how to use Human Cell Atlas data in Terra"},"content":{"rendered":"<p><span style=\"font-weight: 400;\">The <\/span><a href=\"https:\/\/www.humancellatlas.org\/\"><span style=\"font-weight: 400;\">Human Cell Atlas<\/span><\/a><span style=\"font-weight: 400;\"> is an impressive project that brings together a multitude of &#8216;omics datasets generated by over 300 different labs from across the world. Its data collection currently comprises data from 20M cells representing 10 major organs, originating from over 2,300 donors. All of it is publicly accessible, forming a veritable cornucopia of data for anyone seeking to probe the intricacies of our cells and the systems of life.<\/span><\/p>\n<p><span style=\"font-weight: 400;\">What&#8217;s perhaps even more impressive, given the crowd-sourced nature of this enormous collection, is that the bulk of the data contributed to the HCA is additionally re-processed through uniform pipelines and made available in standardized, well-documented formats. This goes a long way toward enabling a wide range of researchers to reuse this data and incorporate it into their own analyses, thus multiplying the value of each bit (or byte?) of data collected.\u00a0<\/span><\/p>\n<p>&nbsp;<\/p>\n<h3>A short hop from the HCA Data Portal to your Terra workspace<\/h3>\n<p><span style=\"font-weight: 400;\">The HCA project makes its collection available through a <\/span><a href=\"https:\/\/data.humancellatlas.org\/\"><span style=\"font-weight: 400;\">Data Portal<\/span><\/a><span style=\"font-weight: 400;\"> that offers multiple options for downloading or otherwise exporting data of interest. My personal favorite (I may be slightly biased) is the option to export metadata to a Terra workspace, from where you can access and analyze the data on the cloud without actually having to download anything.\u00a0<\/span><\/p>\n<p><span style=\"font-weight: 400;\">The export process is relatively straightforward, as you can see in this short 5-min demo video, which goes from browsing the data portal, selecting and exporting a dataset to Terra, to applying some basic analyses using a pre-configured workflow and a Jupyter Notebook running Seurat (<\/span><a href=\"https:\/\/g.co\/doodle\/xkcufs4\"><span style=\"font-weight: 400;\">happy birthday, Georges<\/span><\/a><span style=\"font-weight: 400;\">!).<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><iframe title=\"Using HCA data in Terra\" width=\"800\" height=\"450\" src=\"https:\/\/www.youtube.com\/embed\/G3N2i3NjsfY?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" allowfullscreen><\/iframe><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"font-weight: 400;\">The demo is based on a <\/span><a href=\"https:\/\/app.terra.bio\/#workspaces\/featured-workspaces-hca\/Intro-to-HCA-data-on-Terra\"><span style=\"font-weight: 400;\">tutorial workspace<\/span><\/a><span style=\"font-weight: 400;\"> created by my wonderful colleagues on the Terra User Education team, with expert input from our HCA and Bioconductor project partners, to help researchers get started with HCA data in Terra. The workspace includes pre-imported data from the <\/span><a href=\"https:\/\/data.humancellatlas.org\/explore\/projects\/4d6f6c96-2a83-43d8-8fe1-0f53bffd4674\"><span style=\"font-weight: 400;\">SingleCellLiverLandscape project<\/span><\/a><span style=\"font-weight: 400;\"> (<\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6197289\/\"><span style=\"font-weight: 400;\">MacParland et al., 2018<\/span><\/a><span style=\"font-weight: 400;\">) (which I re-import in the demo so you can see the full end-to-end process) as well as one workflow and four notebooks.\u00a0<\/span><\/p>\n<p><span style=\"font-weight: 400;\">The workflow runs <\/span><a href=\"https:\/\/dockstore.org\/organizations\/BroadInstitute\/collections\/Cumulus\"><span style=\"font-weight: 400;\">Cumulus<\/span><\/a><span style=\"font-weight: 400;\">, a pipeline for analyzing large-scale single-cell and single-nucleus RNA sequencing datasets (<\/span><a href=\"https:\/\/www.nature.com\/articles\/s41592-020-0905-x\"><span style=\"font-weight: 400;\">Li et al. 2020<\/span><\/a><span style=\"font-weight: 400;\">) that takes in a raw count matrix and performs filtering, normalization, and clustering. The four notebooks demonstrate popular single-cell analysis tools including \u200b\u200bBioconductor, Seurat, Scanpy and Pegasus in Terra, with particular focus on providing reusable solutions for accessing and manipulating data on the cloud and for working with the data types and formats provided by the HCA project.<\/span><\/p>\n<p><span style=\"font-weight: 400;\">For more details, have a look at the <\/span><a href=\"https:\/\/support.terra.bio\/hc\/en-us\/articles\/360060041772\"><span style=\"font-weight: 400;\">full text instructions<\/span><\/a><span style=\"font-weight: 400;\"> for the tutorial or <\/span><a href=\"https:\/\/app.terra.bio\/#workspaces\/featured-workspaces-hca\/Intro-to-HCA-data-on-Terra\"><span style=\"font-weight: 400;\">check out the workspace<\/span><\/a><span style=\"font-weight: 400;\"> and take it for a spin yourself \u2014 thanks to this great resource, you can replicate all the steps shown in the demo video, and more, in a matter of minutes! <\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The Human Cell Atlas project makes its vast collection of data available through a Data Portal that offers direct export to a Terra workspace.<\/p>\n","protected":false},"author":4,"featured_media":478,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[12,18,78,31,44,26,119,45,66,59,39,32,14],"tags":[117,99,169,170,171,103,164],"class_list":["post-477","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-analysis","category-data","category-data-access","category-ecosystem","category-interactive-analysis","category-interoperability","category-most-recent","category-notebooks","category-single-cell-transcriptomics","category-single-cell","category-videos","category-workflows","category-workspaces","tag-bioconductor","tag-cumulus","tag-hca","tag-pegasus","tag-scanpy","tag-seurat","tag-single-cell"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.0 - 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