--- a +++ b/docs/articles/index.html @@ -0,0 +1,102 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • deepG</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="https://genomenet.github.io/deepG/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">deepG</a> + + <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">0.3.0</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="nav-item"> + <a class="nav-link" href="../reference/index.html"> + <span class="fa fa fa fa-file-alt"></span> + + Reference + </a> +</li> +<li class="nav-item dropdown"> + <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-notebooks">Notebooks</a> + <div class="dropdown-menu" aria-labelledby="dropdown-notebooks"> + <a class="external-link dropdown-item" href="https://colab.research.google.com/drive/175jIdXcDcgPUvaBo2rH2Lupbpjnp5O7G?usp=sharing">deepG tutorial</a> + <a class="external-link dropdown-item" href="https://colab.research.google.com/drive/1Eolc0koMNM1zkuO4XyVM58ImeF1BpRiH?usp=sharing">Read-length level: Human contamination</a> + <a class="external-link dropdown-item" href="https://colab.research.google.com/drive/1yiXSwFafXpMLHaov9iBTQLIDZ6bK1zYX?usp=sharing">Locus level: CRISPR detection</a> + <a class="external-link dropdown-item" href="https://colab.research.google.com/drive/1G7bOFEX87cZNrM2tdRtTdkrZn5fM__g0?usp=sharing">Gene level: 16S rRNA detection</a> + <a class="external-link dropdown-item" href="https://colab.research.google.com/drive/1BCggL-tfQF136YeJ8cKKi-zoBEDMgkNh?usp=sharing">Genome level: Bacterial morphology (Sporulation)</a> + <a class="external-link dropdown-item" href="https://colab.research.google.com/drive/10xpRzGd3JeBAbqQYSCxzQUMctt01sx9D?usp=sharing">Full metagenome level: Colorectal cancer prediction</a> + <a class="external-link dropdown-item" href="https://colab.research.google.com/drive/1kyYK7IU7GSfdpDzO_a8U3_qD4i3zTu6w?usp=sharing">BERT with deepG</a> + </div> +</li> +<li class="nav-item dropdown"> + <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-tutorials">Tutorials</a> + <div class="dropdown-menu" aria-labelledby="dropdown-tutorials"> + <a class="dropdown-item" href="../articles/getting_started.html">Getting Started</a> + <a class="dropdown-item" href="../articles/training_types.html">Training types</a> + <a class="dropdown-item" href="../articles/data_generator.html">Data generator</a> + <a class="dropdown-item" href="../articles/using_tb.html">Using tensorboard</a> + <a class="dropdown-item" href="../articles/integrated_gradient.html">Integrated Gradient</a> + </div> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/GenomeNet/deepG/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div> + + + </div> +</nav><div class="container template-article-index"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="../logo.png" class="logo" alt=""><h1>Articles</h1> + </div> + + <div class="section "> + <h3>All vignettes</h3> + <div class="section-desc"></div> + + <dl><dt><a href="data_generator.html">Data Generator</a></dt> + <dd> + </dd><dt><a href="getting_started.html">Getting started</a></dt> + <dd> + </dd><dt><a href="integrated_gradient.html">Integrated Gradient</a></dt> + <dd> + </dd><dt><a href="training_types.html">Training Types</a></dt> + <dd> + </dd><dt><a href="using_tb.html">Using Tensorboard</a></dt> + <dd> + </dd></dl></div> + </main></div> + + + <footer><div class="pkgdown-footer-left"> + <p>Developed by Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy.</p> +</div> + +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p> +</div> + + </footer></div> + + + + + + </body></html> +