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Starlitnightly · Jun 30, 2024 · b59e6ca · b59e6ca
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diff --git a/.DS_Store b/.DS_Store
diff --git a/Release_notes/index.html b/Release_notes/index.html
@@ -1219,6 +1219,11 @@
     pl Module
   </a>
 </li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#utils-module_8">
+    utils Module
+  </a>
+</li>
 </ul>
 </nav>
 </li>
@@ -1945,6 +1950,11 @@
     pl Module
   </a>
 </li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#utils-module_8">
+    utils Module
+  </a>
+</li>
 </ul>
 </nav>
 </li>
@@ -2393,11 +2403,13 @@ <h2 id="v-162">v 1.6.2<a class="headerlink" href="#v-162" title="Permanent link"
 <h2 id="v-163">v 1.6.3<a class="headerlink" href="#v-163" title="Permanent link">¶</a></h2>
 <ul>
 <li>Added  <code>ov.setting.cpu_init</code> to change the environment to CPU.</li>
+<li>Move module <code>tape</code>,<code>SEACells</code> and <code>palantir</code> to <code>externel</code></li>
 </ul>
 <h3 id="single-module_26">Single Module<a class="headerlink" href="#single-module_26" title="Permanent link">¶</a></h3>
 <ul>
 <li>Added <code>CytoTrace2</code> to predict cellular potency categories and absolute developmental potential from single-cell RNA-sequencing data.</li>
 <li>Added <code>cpdb_exact_target</code> and <code>cpdb_exact_source</code> to exact the means of special ligand/receptor</li>
+<li>Added <code>gptcelltype_local</code> to identify the celltype using local LLM #96 #99</li>
 </ul>
 <h3 id="bulk-module_9">Bulk Module<a class="headerlink" href="#bulk-module_9" title="Permanent link">¶</a></h3>
 <ul>
@@ -2406,11 +2418,17 @@ <h3 id="bulk-module_9">Bulk Module<a class="headerlink" href="#bulk-module_9" ti
 <h3 id="space-module_6">Space Module<a class="headerlink" href="#space-module_6" title="Permanent link">¶</a></h3>
 <ul>
 <li>Added <code>**kwargs</code> in <code>STT.compute_pathway</code></li>
+<li>Added <code>GraphST</code> to identify the spatial domain</li>
 </ul>
 <h3 id="pl-module_2">pl Module<a class="headerlink" href="#pl-module_2" title="Permanent link">¶</a></h3>
 <ul>
 <li>Added <code>cpdb_network</code>, <code>cpdb_chord</code>, <code>cpdb_heatmap</code>, <code>cpdb_interacting_network</code>,<code>cpdb_interacting_heatmap</code> and <code>cpdb_group_heatmap</code> to visualize the result of CellPhoneDB</li>
 </ul>
+<h3 id="utils-module_8">utils Module<a class="headerlink" href="#utils-module_8" title="Permanent link">¶</a></h3>
+<ul>
+<li>Added <code>mclust_py</code> to identify the Gaussian Mixture cluster</li>
+<li>Added <code>mclust</code> methdo in <code>cluster</code> function</li>
+</ul>
 </article>
 </div>
 </div>

diff --git a/Tutorials-bulk2single/t_bulk2single/index.html b/Tutorials-bulk2single/t_bulk2single/index.html
diff --git a/Tutorials-single/t_gptanno/index.html b/Tutorials-single/t_gptanno/index.html
diff --git a/Tutorials-single/t_metacells/index.html b/Tutorials-single/t_metacells/index.html
diff --git a/Tutorials-single/t_traj/index.html b/Tutorials-single/t_traj/index.html
diff --git a/Tutorials-space/t_stagate/index.html b/Tutorials-space/t_stagate/index.html
diff --git a/api/bulk/api_deseq/index.html b/api/bulk/api_deseq/index.html
diff --git a/api/bulk2single/api_bulk2single/index.html b/api/bulk2single/api_bulk2single/index.html
@@ -635,7 +635,7 @@ <h2 class="doc doc-heading" id="omicverse.bulk2single.Bulk2Single">
 <span class="linenos" data-linenos=" 70 "></span>                        <span class="n">mode</span><span class="o">=</span><span class="s1">'overall'</span><span class="p">,</span> <span class="n">adaptive</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">variance_threshold</span><span class="o">=</span><span class="mf">0.98</span><span class="p">,</span>
 <span class="linenos" data-linenos=" 71 "></span>                        <span class="n">save_model_name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
 <span class="linenos" data-linenos=" 72 "></span>                        <span class="n">batch_size</span><span class="o">=</span><span class="mi">128</span><span class="p">,</span> <span class="n">epochs</span><span class="o">=</span><span class="mi">128</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">scale_size</span><span class="o">=</span><span class="mi">2</span><span class="p">):</span>
-<span class="linenos" data-linenos=" 73 "></span>        <span class="kn">from</span> <span class="nn">..tape</span> <span class="kn">import</span> <span class="n">Deconvolution</span><span class="p">,</span><span class="n">ScadenDeconvolution</span>
+<span class="linenos" data-linenos=" 73 "></span>        <span class="kn">from</span> <span class="nn">..externel.tape</span> <span class="kn">import</span> <span class="n">Deconvolution</span><span class="p">,</span><span class="n">ScadenDeconvolution</span>
 <span class="linenos" data-linenos=" 74 "></span>        <span class="n">sc_ref</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sc_ref</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
 <span class="linenos" data-linenos=" 75 "></span>        <span class="k">if</span> <span class="n">method</span><span class="o">==</span><span class="s1">'scaden'</span><span class="p">:</span>
 <span class="linenos" data-linenos=" 76 "></span>            <span class="n">CellFractionPrediction</span><span class="o">=</span><span class="n">ScadenDeconvolution</span><span class="p">(</span><span class="n">sc_ref</span><span class="p">,</span>