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@Cloufield
Cloufield committed Feb 16, 2024
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<a href="#install-in-conda-environment" class="md-nav__link">
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install in conda environment
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<li class="md-nav__item">
<a href="#install-in-conda-environment" class="md-nav__link">
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install in conda environment
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Expand Down Expand Up @@ -2171,8 +2189,17 @@ <h3 id="install-via-pip">install via pip</h3>
</span><span id="__span-1-25"><a id="__codelineno-1-25" name="__codelineno-1-25" href="#__codelineno-1-25"></a><span class="n">mysumstats</span><span class="o">.</span><span class="n">plot_mqq</span><span class="p">()</span>
</span><span id="__span-1-26"><a id="__codelineno-1-26" name="__codelineno-1-26" href="#__codelineno-1-26"></a><span class="o">...</span>
</span></code></pre></div>
<h3 id="install-in-conda-environment">install in conda environment</h3>
<p>Create a Python 3.9 environment and install gwaslab using pip:</p>
<div class="language-text highlight"><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>conda env create -n gwaslab_test -c conda-forge python=3.9
</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>conda activate gwaslab
</span><span id="__span-2-3"><a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a>pip install gwaslab==3.4.40
</span></code></pre></div>
<p>or create a new environment using yml file <a href="https://github.com/Cloufield/gwaslab/blob/main/environment_3.4.40.yml">environment_3.4.40.yml</a></p>
<div class="language-text highlight"><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>conda env create -n gwaslab -f environment_3.4.40.yml
</span></code></pre></div>
<h3 id="install-using-docker">install using docker</h3>
<p>A docker filer is available <a href="https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile">here</a> for building images.</p>
<p>A docker filer is available <a href="https://github.com/Cloufield/gwaslab/blob/main/docker/Dockerfile">here</a> for building local images.</p>
<h2 id="functions">Functions</h2>
<h3 id="loading-and-formatting">Loading and Formatting</h3>
<ul>
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</ul>
<h2 id="requirements-deprecated">Requirements (deprecated)</h2>
<p>environment.yml</p>
<div class="language-text highlight"><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>name: gwaslab
</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>channels:
</span><span id="__span-2-3"><a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a> - conda-forge
</span><span id="__span-2-4"><a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a> - defaults
</span><span id="__span-2-5"><a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>dependencies:
</span><span id="__span-2-6"><a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a> - python=3.8.16=h7a1cb2a_3
</span><span id="__span-2-7"><a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a> - jupyter==1.0.0
</span><span id="__span-2-8"><a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a> - pip==23.1.2
</span><span id="__span-2-9"><a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a> - pip:
</span><span id="__span-2-10"><a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a> - adjusttext==0.8
</span><span id="__span-2-11"><a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a> - biopython==1.81
</span><span id="__span-2-12"><a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a> - gwaslab==3.4.16
</span><span id="__span-2-13"><a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a> - liftover==1.1.16
</span><span id="__span-2-14"><a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a> - matplotlib==3.7.1
</span><span id="__span-2-15"><a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a> - numpy==1.24.2
</span><span id="__span-2-16"><a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a> - pandas==1.4.4
</span><span id="__span-2-17"><a id="__codelineno-2-17" name="__codelineno-2-17" href="#__codelineno-2-17"></a> - scikit-allel==1.3.5
</span><span id="__span-2-18"><a id="__codelineno-2-18" name="__codelineno-2-18" href="#__codelineno-2-18"></a> - scikit-learn==1.2.2
</span><span id="__span-2-19"><a id="__codelineno-2-19" name="__codelineno-2-19" href="#__codelineno-2-19"></a> - scipy==1.10.1
</span><span id="__span-2-20"><a id="__codelineno-2-20" name="__codelineno-2-20" href="#__codelineno-2-20"></a> - seaborn==0.11.2
</span><span id="__span-2-21"><a id="__codelineno-2-21" name="__codelineno-2-21" href="#__codelineno-2-21"></a> - statsmodels==0.13
</span><span id="__span-2-22"><a id="__codelineno-2-22" name="__codelineno-2-22" href="#__codelineno-2-22"></a> - adjustText==0.8
</span><span id="__span-2-23"><a id="__codelineno-2-23" name="__codelineno-2-23" href="#__codelineno-2-23"></a> - pysam==0.19
</span><span id="__span-2-24"><a id="__codelineno-2-24" name="__codelineno-2-24" href="#__codelineno-2-24"></a> - pyensembl==2.2.3
<div class="language-text highlight"><pre><span></span><code><span id="__span-4-1"><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>name: gwaslab
</span><span id="__span-4-2"><a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>channels:
</span><span id="__span-4-3"><a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a> - conda-forge
</span><span id="__span-4-4"><a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a> - defaults
</span><span id="__span-4-5"><a id="__codelineno-4-5" name="__codelineno-4-5" href="#__codelineno-4-5"></a>dependencies:
</span><span id="__span-4-6"><a id="__codelineno-4-6" name="__codelineno-4-6" href="#__codelineno-4-6"></a> - python=3.8.16=h7a1cb2a_3
</span><span id="__span-4-7"><a id="__codelineno-4-7" name="__codelineno-4-7" href="#__codelineno-4-7"></a> - jupyter==1.0.0
</span><span id="__span-4-8"><a id="__codelineno-4-8" name="__codelineno-4-8" href="#__codelineno-4-8"></a> - pip==23.1.2
</span><span id="__span-4-9"><a id="__codelineno-4-9" name="__codelineno-4-9" href="#__codelineno-4-9"></a> - pip:
</span><span id="__span-4-10"><a id="__codelineno-4-10" name="__codelineno-4-10" href="#__codelineno-4-10"></a> - adjusttext==0.8
</span><span id="__span-4-11"><a id="__codelineno-4-11" name="__codelineno-4-11" href="#__codelineno-4-11"></a> - biopython==1.81
</span><span id="__span-4-12"><a id="__codelineno-4-12" name="__codelineno-4-12" href="#__codelineno-4-12"></a> - gwaslab==3.4.16
</span><span id="__span-4-13"><a id="__codelineno-4-13" name="__codelineno-4-13" href="#__codelineno-4-13"></a> - liftover==1.1.16
</span><span id="__span-4-14"><a id="__codelineno-4-14" name="__codelineno-4-14" href="#__codelineno-4-14"></a> - matplotlib==3.7.1
</span><span id="__span-4-15"><a id="__codelineno-4-15" name="__codelineno-4-15" href="#__codelineno-4-15"></a> - numpy==1.24.2
</span><span id="__span-4-16"><a id="__codelineno-4-16" name="__codelineno-4-16" href="#__codelineno-4-16"></a> - pandas==1.4.4
</span><span id="__span-4-17"><a id="__codelineno-4-17" name="__codelineno-4-17" href="#__codelineno-4-17"></a> - scikit-allel==1.3.5
</span><span id="__span-4-18"><a id="__codelineno-4-18" name="__codelineno-4-18" href="#__codelineno-4-18"></a> - scikit-learn==1.2.2
</span><span id="__span-4-19"><a id="__codelineno-4-19" name="__codelineno-4-19" href="#__codelineno-4-19"></a> - scipy==1.10.1
</span><span id="__span-4-20"><a id="__codelineno-4-20" name="__codelineno-4-20" href="#__codelineno-4-20"></a> - seaborn==0.11.2
</span><span id="__span-4-21"><a id="__codelineno-4-21" name="__codelineno-4-21" href="#__codelineno-4-21"></a> - statsmodels==0.13
</span><span id="__span-4-22"><a id="__codelineno-4-22" name="__codelineno-4-22" href="#__codelineno-4-22"></a> - adjustText==0.8
</span><span id="__span-4-23"><a id="__codelineno-4-23" name="__codelineno-4-23" href="#__codelineno-4-23"></a> - pysam==0.19
</span><span id="__span-4-24"><a id="__codelineno-4-24" name="__codelineno-4-24" href="#__codelineno-4-24"></a> - pyensembl==2.2.3
</span></code></pre></div>
<h2 id="how-to-cite">How to cite</h2>
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