Commit dd8ddce5 authored by Jun Zhao's avatar Jun Zhao
Browse files

add runtime

parent 22c680d7

README.md

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## Installation

The DAseq package can be installed from this GitHub repository.

The DAseq package can be installed from this GitHub repository. Installation of just the DAseq package should not take longer than a minute or two.



```r

devtools::install_github("KlugerLab/DAseq")
@@ -30,3 +30,5 @@ References of DAseq functions can be found [here](https://klugerlab.github.io/DA 
Please check DA-seq [tutorial](https://klugerlab.github.io/DAseq/articles/tutorial.html).



Data used in the tutorial is from [Sade-Feldman, Moshe, et al. (Cell. 2018)](https://www.sciencedirect.com/science/article/pii/S0092867418313941).



DAseq has been tested on MacOS (Catalina, 10.15) and Ubuntu 16.04.

docs/LICENSE-text.html

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      <h1>License</h1>

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<pre>MIT License



Copyright (c) 2020 Jun Zhao



Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:



The above copyright notice and this permission notice shall be included in all

copies or substantial portions of the Software.



THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

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docs/articles/tutorial.html

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<code>plot.embedding</code>, 2D embedding of the data to visualize the results (t-SNE), this is included in the DAseq package as <code>X.2d.melanoma</code>

</li>

</ul>

<p>Runtime for this step with <code>n.runs = 1</code> is less than a minute on a standard laptop, and it will scale linearly with <code>n.runs</code>.</p>

<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">da_cells</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/getDAcells.html">getDAcells</a></span>(

  <span class="kw">X</span> <span class="kw">=</span> <span class="no">X.melanoma</span>,

  <span class="kw">cell.labels</span> <span class="kw">=</span> <span class="no">X.label.melanoma</span>,

docs/index.html

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<div id="installation" class="section level2">

<h2 class="hasAnchor">

<a href="#installation" class="anchor"></a>Installation</h2>

<p>The DAseq package can be installed from this GitHub repository.</p>

<p>The DAseq package can be installed from this GitHub repository. Installation of just the DAseq package should not take longer than a minute or two.</p>

<div class="sourceCode" id="cb1"><pre class="r"><span class="kw pkg">devtools</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/devtools/man/reexports.html">install_github</a></span>(<span class="st">"KlugerLab/DAseq"</span>)</pre></div>

</div>

<div id="references" class="section level2">
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<a href="#usage" class="anchor"></a>Usage</h2>

<p>Please check DA-seq <a href="https://klugerlab.github.io/DAseq/articles/tutorial.html">tutorial</a>.</p>

<p>Data used in the tutorial is from <a href="https://www.sciencedirect.com/science/article/pii/S0092867418313941">Sade-Feldman, Moshe, et al. (Cell. 2018)</a>.</p>

<p>DAseq has been tested on MacOS (Catalina, 10.15) and Ubuntu 16.04.</p>

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