{"__v":0,"_id":"584592c7ba4f1c0f0096932b","category":{"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","_id":"58458b4fba4f1c0f009692bb","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-12-05T15:44:15.650Z","from_sync":false,"order":6,"slug":"datasets-hub","title":"DATASETS HUB"},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","user":"5613e4f8fdd08f2b00437620","version":{"__v":37,"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","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"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-12-05T16:16:07.155Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"examples":{"codes":[]},"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":20,"body":"[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"On this page:\",\n  \"body\": \"* [[ 1 ] Dataset name](#dataset-name)\\n  * [[ 2 ] Query name](#query-name)\\n  * [[ 3 ] Queries](#queries)\\n  * [[ 4 ] Save a query](#save-a-query)\\n  * [[ 5 ] The Search Box](#search)\\n  * [[ 6 ] Count](#count)\\n  * [[ 7 ] Clear All](#clear-all)\\n  * [[ 8 ] Copy files to project](#copy-files-to-project) \\n  * [[ 9 ] Table of results](#table-of-results)\\n  * [[ 10 ] Distribution graphs](#distribution-graphs)\\n  * [[ 11 ] Export query results](#export-query-results)\"\n}\n[/block]\n\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/adc3d67-Screen_Shot_2017-01-16_at_3.57.54_PM.jpg\",\n        \"Screen Shot 2017-01-16 at 3.57.54 PM.jpg\",\n        1600,\n        932,\n        \"#eceded\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n<a name=\"dataset-name\"></a>\n##[ 1 ] Dataset name\n\nThe name of the dataset you are querying is on the left side of the top navigation bar. In the image above, you are currently querying the TCGA dataset.\n\nTo clear your canvas and switch to another dataset (e.g. CCLE,), simply click on the visible dataset name (e.g. TCGA). This opens a dialog in which you can select the alternate dataset.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"query-name\"></a>\n##[ 2 ] Query name\n\nThe name of your query is also on the left side of the top navigation bar. This defaults to **New query** if your query is unsaved.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"queries\"></a>\n##[ 3 ] Queries\n\nClick on **Queries** to reveal different actions relating to queries, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/f458ec2-.jpeg\",\n        \"'.jpeg\",\n        406,\n        342,\n        \"#5d5c5e\"\n      ]\n    }\n  ]\n}\n[/block]\nChoose to create a new query, open a previously saved query, open an example query provided by the CGC team, or save a query.\nLearn more about:\n* [Starting from an example query](doc:data-browser-query-start-from-an-example-query) \n* [Building a query from scratch](doc:data-browser-query-start-from-scratch) \n* [Working from an existing query](doc:data-browser-query-start-from-an-existing-query) \n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"save-a-query\"></a>\n##[ 4 ] Save a query\n\nYou can save any query on the Data Browser. Note that empty canvases cannot be saved as queries.\n\nThis feature is still in Beta, and we will continue to make improvements.\n\nTo save a query:\n1. Click **Queries** on the top of the Data Browser canvas next to the help icon.\n2. Select **Save** from the drop-down menu.\n3. In the pop-up window which appears, you can name your query, as shown below. Click **Add description** to add a brief description of your query.\n4. Then, click **Save Query**.\n\nAll saved queries can be accessed by selecting Existing queries from the Queries drop-down menu. \n\nLearn more about [accessing existing queries](doc:data-browser-query-start-from-an-existing-query).\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"search\"></a>\n##[ 5 ] The Search Box\n\nClick on **Search by ID** to reveal the search box. The search box allows you to search by UUID, ID (TCGA Barcodes), or file name.\n\nYou can enter more than one UUID, ID (TCGA Barcode), or file name (separated by commas) into the search box and click **Search**.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/00e4ad4-pCjCMJJgTch86oJV1Vns_Screen_Shot_2016-05-10_at_4.33.51_PM_1.jpeg\",\n        \"pCjCMJJgTch86oJV1Vns_Screen Shot 2016-05-10 at 4.33.51 PM (1).jpeg\",\n        984,\n        604,\n        \"#e8e8e8\"\n      ]\n    }\n  ]\n}\n[/block]\nFor instance, you can search for **TCGA-OR-A5JW-01A-11D-A29I-10_Illumina.bam.bai**. This will populate the Data Browser with a query starting from the file **TCGA-OR-A5JW-01A-11D-A29I-10_Illumina.bam.bai**. You can use this as the starting point of your query.\n\nIf you mix two types of search terms (such a UUID and file name), you will be asked to choose one\nLearn more about ways to search in the Data Browser.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"count\"></a>\n##[ 6 ] Count\n\nThe Count feature quantifies the scope of the data returned by your query.\n\nA count card at the bottom of the Data Browser displays the entity and number of instances of that entity which satisfy your query. For example, the count card for **Case** shows how many cases are returned by your query.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/09a3cbd-LVkmi6mFTf3ZLkRDDRnG_Screen_Shot_2016-05-25_at_5.11.34_PM.jpeg\",\n        \"LVkmi6mFTf3ZLkRDDRnG_Screen Shot 2016-05-25 at 5.11.34 PM.jpeg\",\n        338,\n        176,\n        \"#e35655\"\n      ]\n    }\n  ]\n}\n[/block]\nThe number of entities returned change as you add filters to your query. The count cards at the bottom of the page gray out to let you know the represented quantities need to be refreshed.\n\nTo refresh the number of instances of each entity returned by your query, click the circular arrows next to the count cards.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"clear-all\"></a>\n##[ 7 ] Clear All\n\nThe trash can icon on the canvas acts a the \"clear all\" button. It allows you to delete all previous queries and opens a new query canvas.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"copy-files-to-project\"></a>\n##[ 8 ] Copy files to project\n\nThe **+Copy files to project** button allows you to copy files that satisfy your query to your desired project. Learn more about [accessing data for use in your project](doc:access-data-from-the-data-browser).\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"table-of-results\"></a>\n##[ 9 ] Table of results\n\nThe **Table of results** below the Data Browser contains a list of UUIDs for the entities which match your query. This table allows you to review returned results, but it does not allow you to select or filter results. All selection and filtering have to be done via the query on the Data Browser canvas.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"distribution-graphs\"></a>\n##[ 10 ] Distribution graphs\nToggle between the **Table of results** and graphs showing the distributions of the members of each entity, as shown below. These graphs are an alternative way to visualize query results and reflects the same information as is displayed in the table.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/930cf2c-Screen_Shot_2017-01-16_at_4.10.14_PM.png\",\n        \"Screen Shot 2017-01-16 at 4.10.14 PM.png\",\n        876,\n        259,\n        \"#8d1fb0\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"export-query-results\"></a>\n##[ 11 ] Export query results\n\nExport query results as a CSV, JSON, or XML file from this table by clicking **Export**. All query results are exported simultaneously but are separated into a different file for each branch. You can only export up to 3000 rows from the table results for each branch.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"<a href=\"query-datasets\" style=\"color:#132c56\">QUERY DATASETS</a> ><a href=\"about-the-data-browser\" style=\"color:#132c56\">About the Data Browser</a> > Data Browser features","slug":"data-browser-features","type":"basic","title":"↳ Data Browser features"}

↳ Data Browser features

<a href="query-datasets" style="color:#132c56">QUERY DATASETS</a> ><a href="about-the-data-browser" style="color:#132c56">About the Data Browser</a> > Data Browser features

[block:callout] { "type": "warning", "title": "On this page:", "body": "* [[ 1 ] Dataset name](#dataset-name)\n * [[ 2 ] Query name](#query-name)\n * [[ 3 ] Queries](#queries)\n * [[ 4 ] Save a query](#save-a-query)\n * [[ 5 ] The Search Box](#search)\n * [[ 6 ] Count](#count)\n * [[ 7 ] Clear All](#clear-all)\n * [[ 8 ] Copy files to project](#copy-files-to-project) \n * [[ 9 ] Table of results](#table-of-results)\n * [[ 10 ] Distribution graphs](#distribution-graphs)\n * [[ 11 ] Export query results](#export-query-results)" } [/block] [block:image] { "images": [ { "image": [ "https://files.readme.io/adc3d67-Screen_Shot_2017-01-16_at_3.57.54_PM.jpg", "Screen Shot 2017-01-16 at 3.57.54 PM.jpg", 1600, 932, "#eceded" ], "border": true } ] } [/block] <a name="dataset-name"></a> ##[ 1 ] Dataset name The name of the dataset you are querying is on the left side of the top navigation bar. In the image above, you are currently querying the TCGA dataset. To clear your canvas and switch to another dataset (e.g. CCLE,), simply click on the visible dataset name (e.g. TCGA). This opens a dialog in which you can select the alternate dataset. <div align="right"><a href="#top">top</a></div> <a name="query-name"></a> ##[ 2 ] Query name The name of your query is also on the left side of the top navigation bar. This defaults to **New query** if your query is unsaved. <div align="right"><a href="#top">top</a></div> <a name="queries"></a> ##[ 3 ] Queries Click on **Queries** to reveal different actions relating to queries, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/f458ec2-.jpeg", "'.jpeg", 406, 342, "#5d5c5e" ] } ] } [/block] Choose to create a new query, open a previously saved query, open an example query provided by the CGC team, or save a query. Learn more about: * [Starting from an example query](doc:data-browser-query-start-from-an-example-query) * [Building a query from scratch](doc:data-browser-query-start-from-scratch) * [Working from an existing query](doc:data-browser-query-start-from-an-existing-query) <div align="right"><a href="#top">top</a></div> <a name="save-a-query"></a> ##[ 4 ] Save a query You can save any query on the Data Browser. Note that empty canvases cannot be saved as queries. This feature is still in Beta, and we will continue to make improvements. To save a query: 1. Click **Queries** on the top of the Data Browser canvas next to the help icon. 2. Select **Save** from the drop-down menu. 3. In the pop-up window which appears, you can name your query, as shown below. Click **Add description** to add a brief description of your query. 4. Then, click **Save Query**. All saved queries can be accessed by selecting Existing queries from the Queries drop-down menu. Learn more about [accessing existing queries](doc:data-browser-query-start-from-an-existing-query). <div align="right"><a href="#top">top</a></div> <a name="search"></a> ##[ 5 ] The Search Box Click on **Search by ID** to reveal the search box. The search box allows you to search by UUID, ID (TCGA Barcodes), or file name. You can enter more than one UUID, ID (TCGA Barcode), or file name (separated by commas) into the search box and click **Search**. [block:image] { "images": [ { "image": [ "https://files.readme.io/00e4ad4-pCjCMJJgTch86oJV1Vns_Screen_Shot_2016-05-10_at_4.33.51_PM_1.jpeg", "pCjCMJJgTch86oJV1Vns_Screen Shot 2016-05-10 at 4.33.51 PM (1).jpeg", 984, 604, "#e8e8e8" ] } ] } [/block] For instance, you can search for **TCGA-OR-A5JW-01A-11D-A29I-10_Illumina.bam.bai**. This will populate the Data Browser with a query starting from the file **TCGA-OR-A5JW-01A-11D-A29I-10_Illumina.bam.bai**. You can use this as the starting point of your query. If you mix two types of search terms (such a UUID and file name), you will be asked to choose one Learn more about ways to search in the Data Browser. <div align="right"><a href="#top">top</a></div> <a name="count"></a> ##[ 6 ] Count The Count feature quantifies the scope of the data returned by your query. A count card at the bottom of the Data Browser displays the entity and number of instances of that entity which satisfy your query. For example, the count card for **Case** shows how many cases are returned by your query. [block:image] { "images": [ { "image": [ "https://files.readme.io/09a3cbd-LVkmi6mFTf3ZLkRDDRnG_Screen_Shot_2016-05-25_at_5.11.34_PM.jpeg", "LVkmi6mFTf3ZLkRDDRnG_Screen Shot 2016-05-25 at 5.11.34 PM.jpeg", 338, 176, "#e35655" ] } ] } [/block] The number of entities returned change as you add filters to your query. The count cards at the bottom of the page gray out to let you know the represented quantities need to be refreshed. To refresh the number of instances of each entity returned by your query, click the circular arrows next to the count cards. <div align="right"><a href="#top">top</a></div> <a name="clear-all"></a> ##[ 7 ] Clear All The trash can icon on the canvas acts a the "clear all" button. It allows you to delete all previous queries and opens a new query canvas. <div align="right"><a href="#top">top</a></div> <a name="copy-files-to-project"></a> ##[ 8 ] Copy files to project The **+Copy files to project** button allows you to copy files that satisfy your query to your desired project. Learn more about [accessing data for use in your project](doc:access-data-from-the-data-browser). <div align="right"><a href="#top">top</a></div> <a name="table-of-results"></a> ##[ 9 ] Table of results The **Table of results** below the Data Browser contains a list of UUIDs for the entities which match your query. This table allows you to review returned results, but it does not allow you to select or filter results. All selection and filtering have to be done via the query on the Data Browser canvas. <div align="right"><a href="#top">top</a></div> <a name="distribution-graphs"></a> ##[ 10 ] Distribution graphs Toggle between the **Table of results** and graphs showing the distributions of the members of each entity, as shown below. These graphs are an alternative way to visualize query results and reflects the same information as is displayed in the table. [block:image] { "images": [ { "image": [ "https://files.readme.io/930cf2c-Screen_Shot_2017-01-16_at_4.10.14_PM.png", "Screen Shot 2017-01-16 at 4.10.14 PM.png", 876, 259, "#8d1fb0" ], "border": true } ] } [/block] <div align="right"><a href="#top">top</a></div> <a name="export-query-results"></a> ##[ 11 ] Export query results Export query results as a CSV, JSON, or XML file from this table by clicking **Export**. All query results are exported simultaneously but are separated into a different file for each branch. You can only export up to 3000 rows from the table results for each branch. <div align="right"><a href="#top">top</a></div>