{"_id":"57dac47f0c5ef00e0019f726","category":{"_id":"5771811e27a5c20e00030dcd","version":"55faf11ba62ba1170021a9aa","__v":0,"project":"55faf11ba62ba1170021a9a7","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-06-27T19:40:14.237Z","from_sync":false,"order":7,"slug":"public-projects","title":"PUBLIC PROJECTS"},"version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":40,"createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"__v":1,"githubsync":"","project":"55faf11ba62ba1170021a9a7","user":"5613e4f8fdd08f2b00437620","parentDoc":null,"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-09-15T15:55:43.136Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":0,"body":"The CGC maintains public projects which act as repositories for examples of specific analyses as well as the associated data and tools you need to replicate these analyses on the CGC.\n\nTo preserve the integrity of the public projects' resources, you only have read permissions for these projects. You can browse through a public project to review the available data, workflows, and tools. To conduct further analyses, you can also make a copy of the entire project or copy specific resources from the public project into your personal projects. At this point, the copied project becomes your own project: you will have full project admin permissions and control over the project. Your actions in your own project will not affect the public project from which you obtained the resources.\n\nPublic projects on the CGC include:\n\n  * [Smart Variant Filtering](doc:smart-variant-filtering) - Smart Variant Filtering (SVF) uses machine learning algorithms trained on features from the existing Genome In A Bottle (GIAB) variant-called samples (HG001-HG005) to perform variant filtering (classification).\n  * [Cancer Cell Line Encyclopedia (CCLE) project](doc:ccle): This project contains data from the Cancer Cell Line Encyclopedia dataset which you can use on the CGC.\n  * [ICGC-TCGA Dream Somatic Mutation Calling Challenge public project](doc:dream-challenge): This project contains data from the ICGC-TCGA DREAM Somatic Mutation Calling – RNA Challenge (SMC-RNA).\n  * [Simons Genome Diversity Project (SGDP) dataset](doc:simons-genome-diversity-project-sgdp-dataset): This project contains data from the Simons Genome Diversity Project dataset which you can use on the CGC.\n  * [Personal Genome Project UK (PGP-UK) pilot dataset](doc:personal-genome-project-uk-pgp-uk-pilot-dataset): This project contains data from the Personal Genome Project UK dataset which you can use on the CGC.\n  * [Data Cruncher Interactive Analyses](https://cgc.sbgenomics.com/u/sevenbridges/data-cruncher-interactive-analyses/): This project contains [interactive analyses](doc:interactive-analysis-on-the-cgc) that can be executed in [Data Cruncher](doc:about-data-cruncher), and are additional resources that help users mitigate some of the challenges related to interpretation of data obtained as a result of secondary analysis. The project contains the following analyses:\n* Ballgown Interactive Analysis\n* VCF Visualization Interactive Analysis\n* Structural Variation Interactive Analysis\n* ChIP-seq Interactive Analysis\n* Microbiome Differential Abundance Analysis\n\nLearn more about accessing public projects below.\n\n##Access public projects\n\nTo access public projects on the CGC:\n\n1. Select **Public projects** from the top navigation bar, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/6afcd9a-public-projects-overview-1.png\",\n        \"public-projects-overview-1.png\",\n        341,\n        382,\n        \"#2b5b9b\"\n      ]\n    }\n  ]\n}\n[/block]\n2. Choose a public project from the drop-down menu.\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"You can also access public projects via the API by using the naming convention of `{project_owner}/{project}`. Locate the project's owner and name from the URL bar on the visual interface. \\n\\nFor instance, the CCLE public project is located at https://cgc.sbgenomics.com/u/sevenbridges/cancer-cell-line-encyclopedia-ccle/. You can refer to the CCLE public project in the API as `sevenbridges/cancer-cell-line-encyclopedia-ccle`.\",\n  \"title\": \"Access public projects via the API\"\n}\n[/block]","excerpt":"","slug":"public-projects","type":"basic","title":"Public projects overview"}

Public projects overview


The CGC maintains public projects which act as repositories for examples of specific analyses as well as the associated data and tools you need to replicate these analyses on the CGC. To preserve the integrity of the public projects' resources, you only have read permissions for these projects. You can browse through a public project to review the available data, workflows, and tools. To conduct further analyses, you can also make a copy of the entire project or copy specific resources from the public project into your personal projects. At this point, the copied project becomes your own project: you will have full project admin permissions and control over the project. Your actions in your own project will not affect the public project from which you obtained the resources. Public projects on the CGC include: * [Smart Variant Filtering](doc:smart-variant-filtering) - Smart Variant Filtering (SVF) uses machine learning algorithms trained on features from the existing Genome In A Bottle (GIAB) variant-called samples (HG001-HG005) to perform variant filtering (classification). * [Cancer Cell Line Encyclopedia (CCLE) project](doc:ccle): This project contains data from the Cancer Cell Line Encyclopedia dataset which you can use on the CGC. * [ICGC-TCGA Dream Somatic Mutation Calling Challenge public project](doc:dream-challenge): This project contains data from the ICGC-TCGA DREAM Somatic Mutation Calling – RNA Challenge (SMC-RNA). * [Simons Genome Diversity Project (SGDP) dataset](doc:simons-genome-diversity-project-sgdp-dataset): This project contains data from the Simons Genome Diversity Project dataset which you can use on the CGC. * [Personal Genome Project UK (PGP-UK) pilot dataset](doc:personal-genome-project-uk-pgp-uk-pilot-dataset): This project contains data from the Personal Genome Project UK dataset which you can use on the CGC. * [Data Cruncher Interactive Analyses](https://cgc.sbgenomics.com/u/sevenbridges/data-cruncher-interactive-analyses/): This project contains [interactive analyses](doc:interactive-analysis-on-the-cgc) that can be executed in [Data Cruncher](doc:about-data-cruncher), and are additional resources that help users mitigate some of the challenges related to interpretation of data obtained as a result of secondary analysis. The project contains the following analyses: * Ballgown Interactive Analysis * VCF Visualization Interactive Analysis * Structural Variation Interactive Analysis * ChIP-seq Interactive Analysis * Microbiome Differential Abundance Analysis Learn more about accessing public projects below. ##Access public projects To access public projects on the CGC: 1. Select **Public projects** from the top navigation bar, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/6afcd9a-public-projects-overview-1.png", "public-projects-overview-1.png", 341, 382, "#2b5b9b" ] } ] } [/block] 2. Choose a public project from the drop-down menu. [block:callout] { "type": "info", "body": "You can also access public projects via the API by using the naming convention of `{project_owner}/{project}`. Locate the project's owner and name from the URL bar on the visual interface. \n\nFor instance, the CCLE public project is located at https://cgc.sbgenomics.com/u/sevenbridges/cancer-cell-line-encyclopedia-ccle/. You can refer to the CCLE public project in the API as `sevenbridges/cancer-cell-line-encyclopedia-ccle`.", "title": "Access public projects via the API" } [/block]