Commit c641a7ab authored by aditya.bhagwat's avatar aditya.bhagwat
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pkgdown::build_site()

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......@@ -18,17 +18,4 @@
BiocManager::install('BSgenome.Mmusculus.UCSC.mm10')
BiocManager::install('BSgenome.Hsapiens.UCSC.hg38')
index_genome(BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10)
index_genome(BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38)
### Use
# Parallel Targeting
reticulate::use_condaenv('azienv')
bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
bedfile <- system.file('extdata/SRF.bed', package='multicrispr')
targets <- multicrispr::bed_to_granges(bedfile, genome='mm10')
extended <- extend(targets, -22, +22)
spacers <- extended %>% find_spacers(bsgenome)
spacers %<>% add_specificity(extended, bsgenome)
spacers %<>% add_efficiency(bsgenome, method = 'Doench2016')
\ No newline at end of file
index_genome(BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38)
\ No newline at end of file
......@@ -8,11 +8,13 @@
<title>Page not found (404) • multicrispr</title>
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......@@ -63,7 +67,7 @@
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<span class="navbar-brand">
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
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......@@ -77,21 +81,8 @@
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......@@ -120,11 +111,11 @@ Content not found. Please use links in the navbar.
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......@@ -8,11 +8,13 @@
<title>Authors • multicrispr</title>
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......@@ -63,7 +67,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">multicrispr</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
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......@@ -77,21 +81,8 @@
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......@@ -116,31 +107,27 @@
</p>
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<li>
<p><strong>Mette Bentsen</strong>. Author.
</p>
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<p><strong>Jens Preussner</strong>. Author.
<p><strong>Johannes Graumann</strong>. Scientific advisor.
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<p><strong>Mario Looso</strong>. Author.
<p><strong>Mette Bentsen</strong>. Contributor.
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<p><strong>Manuel Kaulich</strong>. Contributor.
<p><strong>Jens Preussner</strong>. Contributor.
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<p><strong>Martin Wegner</strong>. Contributor.
<p><strong>Michael Lawrence</strong>. Contributor.
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<p><strong>Marie Hebel</strong>. Contributor.
<p><strong>Herve Pages</strong>. Contributor.
</p>
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<li>
<p><strong>Johannes Graumann</strong>. Contributor.
<p><strong>Mario Looso</strong>. Scientific advisor, research team head.
</p>
</li>
</ul>
......@@ -153,11 +140,11 @@
<footer>
<div class="copyright">
<p>Developed by Aditya Bhagwat, Mette Bentsen, Jens Preussner, Mario Looso.</p>
<p>Developed by Aditya Bhagwat.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9100.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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......@@ -5,13 +5,13 @@
<meta charset="utf-8">
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<title>Multi-locus crispr design • multicrispr</title>
<title>Multi-locus multi-purpose Crispr/Cas design • multicrispr</title>
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous">
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<meta property="og:description" content="Contains functions to facilitate the design of a multi-locus crispr/cas9 library.">
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<meta property="og:description" content="Contains functions to facilitate the design of a multi-locus Crispr/Cas library.">
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<span class="navbar-brand">
<a class="navbar-link" href="index.html">multicrispr</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.0</span>
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......@@ -45,18 +45,6 @@
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......@@ -73,36 +61,31 @@
<div class="contents col-md-9">
<center> <div class="page-header"><h1> multicrispr </h1></div> </center>
<p><img src="https://gitlab.gwdg.de/loosolab/software/multicrispr/wikis/uploads/43b432cd32eb156af2ac217efd98aceb/workflow.png"></p>
<ol>
<li><p>Read a set of genomics ranges</p></li>
<li>
<p>Find cas9 sequences which</p>
<ul>
<li>
<p>target</p>
<ul>
<li>
<strong>thousands</strong> of such <strong>ranges</strong>, their <strong>flanks</strong>, or <strong>slopped extensions</strong>
</li>
<li>
<strong>efficiently</strong> with <strong>data.table</strong> and <strong>Biostrings</strong> based <strong>c-level</strong> looping and matching</li>
<li>enabling <strong>crispr<sub>ko</sub></strong>, <strong>crispr<sub>i</sub></strong>, and <strong>crispr<sub>a</sub></strong> design.</li>
</ul>
</li>
<li><p>are free of offtarget (mis)matches</p></li>
<li>
<p>bind well</p>
<ul>
<li>as determined by Doench 2016 ontargetscore (interfacing to original python module <strong>azimuth</strong> when available)</li>
<li>or Doench 2014 ontargetscore otherwise</li>
</ul>
</li>
</ul>
</li>
</ol>
<div id="overview" class="section level3">
<h3 class="hasAnchor">
<a href="#overview" class="anchor"></a>Overview</h3>
<p><img src="https://gitlab.gwdg.de/loosolab/software/multicrispr/wikis/uploads/ff69d25a1cad1f4c93fdf79e0c549ecf/readme.png"></p>
</div>
<div id="installation" class="section level3">
<h3 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h3>
<div class="sourceCode" id="cb1"><pre class="sourceCode R"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="co"># Install multicrispr</span></a>
<a class="sourceLine" id="cb1-2" title="2"> remotes<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/remotes/man/install_git.html">install_git</a></span>(<span class="st">'https://gitlab.gwdg.de/loosolab/software/multicrispr.git'</span>, </a>
<a class="sourceLine" id="cb1-3" title="3"> <span class="dt">repos =</span> BiocManager<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/BiocManager/man/repositories.html">repositories</a></span>())</a>
<a class="sourceLine" id="cb1-4" title="4"><span class="co"># Install azimuth</span></a>
<a class="sourceLine" id="cb1-5" title="5"> <span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">'reticulate'</span>)</a>
<a class="sourceLine" id="cb1-6" title="6"> reticulate<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/reticulate/man/conda-tools.html">conda_create</a></span>(<span class="st">'azienv'</span>, <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">'python=2.7'</span>))</a>
<a class="sourceLine" id="cb1-7" title="7"> reticulate<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/reticulate/man/use_python.html">use_condaenv</a></span>(<span class="st">'azienv'</span>)</a>
<a class="sourceLine" id="cb1-8" title="8"> reticulate<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/reticulate/man/py_install.html">py_install</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">'azimuth'</span>, <span class="st">'scikit-learn==0.17.1'</span>), <span class="st">'azienv'</span>, <span class="dt">pip =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb1-9" title="9"><span class="co"># Index mm10 and hg38</span></a>
<a class="sourceLine" id="cb1-10" title="10"> BiocManager<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/BiocManager/man/install.html">install</a></span>(<span class="st">'BSgenome.Mmusculus.UCSC.mm10'</span>)</a>
<a class="sourceLine" id="cb1-11" title="11"> BiocManager<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/BiocManager/man/install.html">install</a></span>(<span class="st">'BSgenome.Hsapiens.UCSC.hg38'</span>)</a>
<a class="sourceLine" id="cb1-12" title="12"> <span class="kw"><a href="reference/index_genome.html">index_genome</a></span>(BSgenome.Mmusculus.UCSC.mm10<span class="op">::</span>BSgenome.Mmusculus.UCSC.mm10)</a>
<a class="sourceLine" id="cb1-13" title="13"> <span class="kw"><a href="reference/index_genome.html">index_genome</a></span>(BSgenome.Hsapiens.UCSC.hg38<span class="op">::</span>BSgenome.Hsapiens.UCSC.hg38)</a></code></pre></div>
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<h2>License</h2>
......@@ -114,9 +97,6 @@
<h2>Developers</h2>
<ul class="list-unstyled">
<li>Aditya Bhagwat <br><small class="roles"> Author, maintainer </small> </li>
<li>Mette Bentsen <br><small class="roles"> Author </small> </li>
<li>Jens Preussner <br><small class="roles"> Author </small> </li>
<li>Mario Looso <br><small class="roles"> Author </small> </li>
<li><a href="authors.html">All authors...</a></li>
</ul>
</div>
......@@ -126,11 +106,11 @@
<footer><div class="copyright">
<p>Developed by Aditya Bhagwat, Mette Bentsen, Jens Preussner, Mario Looso.</p>
<p>Developed by Aditya Bhagwat.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9100.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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pkgdown_sha: 1829398a4e97056fe7fb332d0e8b952784b49321
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<h1>Get EnsDb.Hsapiens.v98 from AnnotationHub</h1>
<div class="hidden name"><code>EnsDb.Hsapiens.v99.Rd</code></div>
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<p>Get EnsDb.Hsapiens.v98 from AnnotationHub</p>
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<pre class="usage"><span class='fu'>EnsDb.Hsapiens.v99</span>()</pre>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p><code><a href='https://rdrr.io/pkg/ensembldb/man/EnsDb-class.html'>EnsDb-class</a></code></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fu'>EnsDb.Hsapiens.v99</span>()</div><div class='output co'>#&gt; <span class='message'>snapshotDate(): 2019-10-29</span></div><div class='output co'>#&gt; <span class='message'>loading from cache</span></div><div class='output co'>#&gt; <span class='message'>require("ensembldb")</span></div><div class='output co'>#&gt; EnsDb for Ensembl:
#&gt; |Backend: SQLite
#&gt; |Db type: EnsDb
#&gt; |Type of Gene ID: Ensembl Gene ID
#&gt; |Supporting package: ensembldb
#&gt; |Db created by: ensembldb package from Bioconductor
#&gt; |script_version: 0.3.5
#&gt; |Creation time: Mon Feb 3 13:20:00 2020
#&gt; |ensembl_version: 99
#&gt; |ensembl_host: localhost
#&gt; |Organism: Homo sapiens
#&gt; |taxonomy_id: 9606
#&gt; |genome_build: GRCh38
#&gt; |DBSCHEMAVERSION: 2.1
#&gt; | No. of genes: 67998.
#&gt; | No. of transcripts: 250641.
#&gt; |Protein data available.</div></pre>
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