Skip to content

Commit

Permalink
Refreshes Retype-generated documentation.
Browse files Browse the repository at this point in the history
Process triggered by alexeliotlash.
  • Loading branch information
Retype GitHub Action committed Oct 12, 2023
1 parent 3f6af30 commit 8d73c4f
Show file tree
Hide file tree
Showing 27 changed files with 122 additions and 104 deletions.
8 changes: 4 additions & 4 deletions 404.html
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.749060582445">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.750441365593">

<!-- See retype.com -->
<meta name="generator" content="Retype 3.5.0">
Expand All @@ -27,11 +27,11 @@

<script data-cfasync="false">(function () { var el = document.documentElement, m = localStorage.getItem("doc_theme"), wm = window.matchMedia; if (m === "dark" || (!m && wm && wm("(prefers-color-scheme: dark)").matches)) { el.classList.add("dark") } else { el.classList.remove("dark") } })();</script>

<link href="/resources/css/retype.css?v=3.5.0.749060582445" rel="stylesheet">
<link href="/resources/css/retype.css?v=3.5.0.750441365593" rel="stylesheet">

<script data-cfasync="false" src="/resources/js/config.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="/resources/js/config.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="/resources/js/retype.js?v=3.5.0" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="/resources/js/lunr.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="/resources/js/lunr.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
</head>
<body>
<div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
Expand Down
38 changes: 28 additions & 10 deletions access_controlled/cds_access/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,15 @@
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.749060582445">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.750441365593">

<!-- See retype.com -->
<meta name="generator" content="Retype 3.5.0">

<!-- Primary Meta Tags -->
<title>NCI&#39;s Cancer Data Service</title>
<meta name="title" content="NCI's Cancer Data Service">
<meta name="description" content="The CDS Portal, within NCI's Cancer Research Data Commons (CRDC), provides access to both open and controlled access data.">
<meta name="description" content="The CDS Portal, within NCI's Cancer Research Data Commons (CRDC), provides an interface to filter and select data from a variety of NCI programs,...">

<!-- Canonical -->
<link rel="canonical" href="/access_controlled/cds_access/">
Expand All @@ -20,21 +20,21 @@
<meta property="og:type" content="website">
<meta property="og:url" content="/access_controlled/cds_access/">
<meta property="og:title" content="NCI's Cancer Data Service">
<meta property="og:description" content="The CDS Portal, within NCI's Cancer Research Data Commons (CRDC), provides access to both open and controlled access data.">
<meta property="og:description" content="The CDS Portal, within NCI's Cancer Research Data Commons (CRDC), provides an interface to filter and select data from a variety of NCI programs,...">

<!-- Twitter -->
<meta property="twitter:card" content="summary_large_image">
<meta property="twitter:url" content="/access_controlled/cds_access/">
<meta property="twitter:title" content="NCI's Cancer Data Service">
<meta property="twitter:description" content="The CDS Portal, within NCI's Cancer Research Data Commons (CRDC), provides access to both open and controlled access data.">
<meta property="twitter:description" content="The CDS Portal, within NCI's Cancer Research Data Commons (CRDC), provides an interface to filter and select data from a variety of NCI programs,...">

<script data-cfasync="false">(function () { var el = document.documentElement, m = localStorage.getItem("doc_theme"), wm = window.matchMedia; if (m === "dark" || (!m && wm && wm("(prefers-color-scheme: dark)").matches)) { el.classList.add("dark") } else { el.classList.remove("dark") } })();</script>

<link href="../../resources/css/retype.css?v=3.5.0.749060582445" rel="stylesheet">
<link href="../../resources/css/retype.css?v=3.5.0.750441365593" rel="stylesheet">

<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/retype.js?v=3.5.0" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
</head>
<body>
<div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
Expand Down Expand Up @@ -169,9 +169,27 @@ <h1>
<span>NCI&#x27;s Cancer Data Service</span>
</h1>
</doc-anchor-target>
<p>The <a href="https://dataservice.datacommons.cancer.gov/">CDS Portal</a>, within NCI&#x27;s Cancer Research Data Commons (CRDC), provides access to both open and controlled access data.</p>
<p>CDS currently hosts a variety of data types from NCI projects, including those from the <a href="https://dataservice.datacommons.cancer.gov/#/study/phs002371">Human Tumor Atlas Network</a>.</p>
<p>dbGaP approval for HTAN study <a href="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002371.v3.p1">phs002371</a> is required in order to access HTAN lower-level genomics data, such as RNAseq FASTQ and BAM files.</p>
<p>The <a href="https://dataservice.datacommons.cancer.gov/">CDS Portal</a>, within NCI&#x27;s Cancer Research Data Commons (CRDC), provides an interface to filter and select data from a variety of NCI programs, including controlled-access, primary sequence data from the Human Tumor Atlas Network (HTAN).</p>
<p>In order to access these HTAN data within the <a href="https://dataservice.datacommons.cancer.gov/">CDS Portal</a>, navigate to the portal in a web browser and click on the <strong>Explore CDS Data</strong> button on the landing page.</p>
<p align="center"><img width="364" alt="1" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/40aff1af-a58f-49dc-9253-6ee5e67ef419">
</p>
<p> </p>
<p>On the Data Explorer page, expand the STUDY section on the left sidebar, scroll down, and check the box next to <strong>Human Tumor Atlas (HTAN) primary sequence data</strong>.</p>
<p align="center"><img width="891" alt="Figure 2" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/4a3b97f6-97d6-4c99-b782-88c9a8a74fba"></p>
<p> </p>
<p>This action will change the summary panel to reflect selecting HTAN data only.</p>
<p align="center"><img width="891" alt="Figure 3" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/14e07c72-16d4-463a-b8b2-1ef5f8d72107"></p>
<p> </p>
<p>Scroll down, or click on the <strong>Collapse View</strong> tab on the upper right just below the query summary line in order to see the tabulated view of all of the participants, samples or files in HTAN.</p>
<p align="center"><img width="891" alt="Figure 4" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/87e90271-a525-4ff7-baeb-4c75ea073a91"></p>
<p> </p>
<p>Click on the <strong>Add All Files</strong> button, or select the check boxes next to all Participants, Samples or Files for a subselection and then click on the <strong>Add Selected</strong> button. This action will update your cart icon in the upper right corner.</p>
<p align="center"><img width="891" alt="Figure 5" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/e79dd76d-8eb1-460f-8957-0e07b3898845"></p>
<p> </p>
<p>Clicking on the cart icon, will bring up a list of the selected files. Click on the <strong>Download Manifest</strong> button in the upper right to download a CSV-formated (Excel compatible) file of this file list.</p>
<p align="center"><img width="891" alt="Figure 6" src="https://github.com/ncihtan/htan_missing_manual/assets/123744798/d3addd28-652d-4320-a109-d0080d1d37df"></p>
<p> </p>
<p>Once this file manifest is downloaded, it will have to be uploaded into your <a href="https://www.cancergenomicscloud.org/">Seven Bridges Cancer Genomics Cloud</a> account, in order for you to be able to download, or otherwise compute on, these data. <strong>NOTE</strong>: dbGaP approval for HTAN study <a href="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002371.v3.p1">phs002371</a> is required in order to access HTAN lower-level genomics data, such as RNAseq FASTQ and BAM files.</p>


<!-- Required only on API pages -->
Expand Down
8 changes: 4 additions & 4 deletions access_controlled/db_gap/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.749060582445">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.750441365593">

<!-- See retype.com -->
<meta name="generator" content="Retype 3.5.0">
Expand All @@ -30,11 +30,11 @@

<script data-cfasync="false">(function () { var el = document.documentElement, m = localStorage.getItem("doc_theme"), wm = window.matchMedia; if (m === "dark" || (!m && wm && wm("(prefers-color-scheme: dark)").matches)) { el.classList.add("dark") } else { el.classList.remove("dark") } })();</script>

<link href="../../resources/css/retype.css?v=3.5.0.749060582445" rel="stylesheet">
<link href="../../resources/css/retype.css?v=3.5.0.750441365593" rel="stylesheet">

<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/retype.js?v=3.5.0" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
</head>
<body>
<div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
Expand Down
8 changes: 4 additions & 4 deletions access_controlled/introduction/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.749060582445">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.750441365593">

<!-- See retype.com -->
<meta name="generator" content="Retype 3.5.0">
Expand All @@ -30,11 +30,11 @@

<script data-cfasync="false">(function () { var el = document.documentElement, m = localStorage.getItem("doc_theme"), wm = window.matchMedia; if (m === "dark" || (!m && wm && wm("(prefers-color-scheme: dark)").matches)) { el.classList.add("dark") } else { el.classList.remove("dark") } })();</script>

<link href="../../resources/css/retype.css?v=3.5.0.749060582445" rel="stylesheet">
<link href="../../resources/css/retype.css?v=3.5.0.750441365593" rel="stylesheet">

<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/retype.js?v=3.5.0" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
</head>
<body>
<div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
Expand Down
8 changes: 4 additions & 4 deletions data_model/biospecimens/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.749060582445">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.750441365593">

<!-- See retype.com -->
<meta name="generator" content="Retype 3.5.0">
Expand All @@ -30,11 +30,11 @@

<script data-cfasync="false">(function () { var el = document.documentElement, m = localStorage.getItem("doc_theme"), wm = window.matchMedia; if (m === "dark" || (!m && wm && wm("(prefers-color-scheme: dark)").matches)) { el.classList.add("dark") } else { el.classList.remove("dark") } })();</script>

<link href="../../resources/css/retype.css?v=3.5.0.749060582445" rel="stylesheet">
<link href="../../resources/css/retype.css?v=3.5.0.750441365593" rel="stylesheet">

<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/retype.js?v=3.5.0" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
</head>
<body>
<div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
Expand Down
8 changes: 4 additions & 4 deletions data_model/clinical/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.749060582445">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.750441365593">

<!-- See retype.com -->
<meta name="generator" content="Retype 3.5.0">
Expand All @@ -30,11 +30,11 @@

<script data-cfasync="false">(function () { var el = document.documentElement, m = localStorage.getItem("doc_theme"), wm = window.matchMedia; if (m === "dark" || (!m && wm && wm("(prefers-color-scheme: dark)").matches)) { el.classList.add("dark") } else { el.classList.remove("dark") } })();</script>

<link href="../../resources/css/retype.css?v=3.5.0.749060582445" rel="stylesheet">
<link href="../../resources/css/retype.css?v=3.5.0.750441365593" rel="stylesheet">

<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/retype.js?v=3.5.0" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
</head>
<body>
<div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
Expand Down
8 changes: 4 additions & 4 deletions data_model/identifiers/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.749060582445">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.750441365593">

<!-- See retype.com -->
<meta name="generator" content="Retype 3.5.0">
Expand Down Expand Up @@ -32,11 +32,11 @@

<script data-cfasync="false">(function () { var el = document.documentElement, m = localStorage.getItem("doc_theme"), wm = window.matchMedia; if (m === "dark" || (!m && wm && wm("(prefers-color-scheme: dark)").matches)) { el.classList.add("dark") } else { el.classList.remove("dark") } })();</script>

<link href="../../resources/css/retype.css?v=3.5.0.749060582445" rel="stylesheet">
<link href="../../resources/css/retype.css?v=3.5.0.750441365593" rel="stylesheet">

<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/retype.js?v=3.5.0" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
</head>
<body>
<div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
Expand Down
8 changes: 4 additions & 4 deletions data_model/imaging/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.749060582445">
<meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.750441365593">

<!-- See retype.com -->
<meta name="generator" content="Retype 3.5.0">
Expand All @@ -30,11 +30,11 @@

<script data-cfasync="false">(function () { var el = document.documentElement, m = localStorage.getItem("doc_theme"), wm = window.matchMedia; if (m === "dark" || (!m && wm && wm("(prefers-color-scheme: dark)").matches)) { el.classList.add("dark") } else { el.classList.remove("dark") } })();</script>

<link href="../../resources/css/retype.css?v=3.5.0.749060582445" rel="stylesheet">
<link href="../../resources/css/retype.css?v=3.5.0.750441365593" rel="stylesheet">

<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/config.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
<script data-cfasync="false" src="../../resources/js/retype.js?v=3.5.0" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.749060582445" data-turbo-eval="false" defer></script>
<script id="lunr-js" data-cfasync="false" src="../../resources/js/lunr.js?v=3.5.0.750441365593" data-turbo-eval="false" defer></script>
</head>
<body>
<div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
Expand Down
Loading

0 comments on commit 8d73c4f

Please sign in to comment.