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@dosumis
dosumis committed Feb 8, 2024
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<div itemprop="articleBody">

<h1>All modules for which code is available</h1>
<ul><li><a href="pandasaurus_cxg/anndata_analyzer.html">pandasaurus_cxg.anndata_analyzer</a></li>
<li><a href="pandasaurus_cxg/anndata_enricher.html">pandasaurus_cxg.anndata_enricher</a></li>
<li><a href="pandasaurus_cxg/enrichment_analysis.html">pandasaurus_cxg.enrichment_analysis</a></li>
<li><a href="pandasaurus_cxg/graph_generator/graph_generator.html">pandasaurus_cxg.graph_generator.graph_generator</a></li>
<li><a href="pandasaurus_cxg/graph_generator/graph_generator_utils.html">pandasaurus_cxg.graph_generator.graph_generator_utils</a></li>
<ul><li><a href="pandasaurus_cxg/graph_generator/graph_generator_utils.html">pandasaurus_cxg.graph_generator.graph_generator_utils</a></li>
<li><a href="pandasaurus_cxg/utils/anndata_loader.html">pandasaurus_cxg.utils.anndata_loader</a></li>
<li><a href="pandasaurus_cxg/utils/exceptions.html">pandasaurus_cxg.utils.exceptions</a></li>
</ul>
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130 changes: 3 additions & 127 deletions genindex.html
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<h1 id="index">Index</h1>

<div class="genindex-jumpbox">
<a href="#_"><strong>_</strong></a>
| <a href="#A"><strong>A</strong></a>
<a href="#A"><strong>A</strong></a>
| <a href="#C"><strong>C</strong></a>
| <a href="#E"><strong>E</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#I"><strong>I</strong></a>
| <a href="#L"><strong>L</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#V"><strong>V</strong></a>

</div>
<h2 id="_">_</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/anndata_analyzer.html#pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer._anndata">_anndata (pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer attribute)</a>
</li>
</ul></td>
</tr></table>

<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/graph_generator/graph_generator_utils.html#pandasaurus_cxg.graph_generator.graph_generator_utils.add_outgoing_edges_to_subgraph">add_outgoing_edges_to_subgraph() (in module pandasaurus_cxg.graph_generator.graph_generator_utils)</a>
</li>
<li><a href="pandasaurus_cxg/anndata_analyzer.html#pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer.all_cell_type_identifiers">all_cell_type_identifiers (pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer attribute)</a>
</li>
<li><a href="pandasaurus_cxg/anndata_analyzer.html#pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer">AnndataAnalyzer (class in pandasaurus_cxg.anndata_analyzer)</a>
</li>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher">AnndataEnricher (class in pandasaurus_cxg.anndata_enricher)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/enrichment_analysis.html#pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer">AnndataEnrichmentAnalyzer (class in pandasaurus_cxg.enrichment_analysis)</a>
</li>
<li><a href="pandasaurus_cxg/utils/anndata_loader.html#pandasaurus_cxg.utils.anndata_loader.AnndataLoader">AnndataLoader (class in pandasaurus_cxg.utils.anndata_loader)</a>
</li>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.annotate_anndata_with_cell_type">annotate_anndata_with_cell_type() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)</a>

<ul>
<li><a href="pandasaurus_cxg/enrichment_analysis.html#pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer.annotate_anndata_with_cell_type">(pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)</a>
</li>
</ul></li>
</ul></td>
</tr></table>

Expand All @@ -126,79 +100,13 @@ <h2 id="C">C</h2>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/utils/exception.html#pandasaurus_cxg.utils.exceptions.CellTypeNotFoundError">CellTypeNotFoundError</a>
</li>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.check_subclass_relationships">check_subclass_relationships() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)</a>
</li>
<li><a href="pandasaurus_cxg/anndata_analyzer.html#pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer.co_annotation_report">co_annotation_report() (pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer method)</a>

<ul>
<li><a href="pandasaurus_cxg/enrichment_analysis.html#pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer.co_annotation_report">(pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.contextual_slim_enrichment">contextual_slim_enrichment() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)</a>

<ul>
<li><a href="pandasaurus_cxg/enrichment_analysis.html#pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer.contextual_slim_enrichment">(pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)</a>
</li>
</ul></li>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.create_cell_type_dict">create_cell_type_dict() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)</a>
</li>
</ul></td>
</tr></table>

<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/graph_generator/graph_generator.html#pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator.enrich_rdf_graph">enrich_rdf_graph() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/anndata_analyzer.html#pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer.enriched_co_annotation_report">enriched_co_annotation_report() (pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer method)</a>

<ul>
<li><a href="pandasaurus_cxg/enrichment_analysis.html#pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer.enriched_co_annotation_report">(pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)</a>
</li>
</ul></li>
</ul></td>
</tr></table>

<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.filter_anndata_with_enriched_cell_type">filter_anndata_with_enriched_cell_type() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)</a>

<ul>
<li><a href="pandasaurus_cxg/enrichment_analysis.html#pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer.filter_anndata_with_enriched_cell_type">(pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)</a>
</li>
</ul></li>
<li><a href="pandasaurus_cxg/graph_generator/graph_generator_utils.html#pandasaurus_cxg.graph_generator.graph_generator_utils.find_and_rotate_center_layout">find_and_rotate_center_layout() (in module pandasaurus_cxg.graph_generator.graph_generator_utils)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/anndata_analyzer.html#pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer.from_file_path">from_file_path() (pandasaurus_cxg.anndata_analyzer.AnndataAnalyzer static method)</a>

<ul>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.from_file_path">(pandasaurus_cxg.anndata_enricher.AnndataEnricher static method)</a>
</li>
</ul></li>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.full_slim_enrichment">full_slim_enrichment() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)</a>

<ul>
<li><a href="pandasaurus_cxg/enrichment_analysis.html#pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer.full_slim_enrichment">(pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)</a>
</li>
</ul></li>
</ul></td>
</tr></table>

<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/graph_generator/graph_generator.html#pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator.generate_rdf_graph">generate_rdf_graph() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/graph_generator/graph_generator.html#pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator">GraphGenerator (class in pandasaurus_cxg.graph_generator.graph_generator)</a>
</li>
</ul></td>
</tr></table>
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<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.minimal_slim_enrichment">minimal_slim_enrichment() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)</a>

<ul>
<li><a href="pandasaurus_cxg/enrichment_analysis.html#pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer.minimal_slim_enrichment">(pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)</a>
</li>
</ul></li>
<li><a href="pandasaurus_cxg/utils/exception.html#pandasaurus_cxg.utils.exceptions.MissingAnalysisProcess">MissingAnalysisProcess</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/utils/exception.html#pandasaurus_cxg.utils.exceptions.MissingEnrichmentProcess">MissingEnrichmentProcess</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
module

Expand Down Expand Up @@ -275,37 +177,11 @@ <h2 id="P">P</h2>
<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/graph_generator/graph_generator.html#pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator.save_rdf_graph">save_rdf_graph() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method)</a>
</li>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.set_enricher_property_list">set_enricher_property_list() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)</a>
</li>
<li><a href="pandasaurus_cxg/graph_generator/graph_generator.html#pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator.set_label_adding_priority">set_label_adding_priority() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.simple_enrichment">simple_enrichment() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)</a>

<ul>
<li><a href="pandasaurus_cxg/enrichment_analysis.html#pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer.simple_enrichment">(pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)</a>
</li>
</ul></li>
<li><a href="pandasaurus_cxg/utils/exception.html#pandasaurus_cxg.utils.exceptions.SubclassWarning">SubclassWarning</a>
</li>
</ul></td>
</tr></table>

<h2 id="V">V</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/anndata_enricher.html#pandasaurus_cxg.anndata_enricher.AnndataEnricher.validate_slim_list">validate_slim_list() (pandasaurus_cxg.anndata_enricher.AnndataEnricher method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="pandasaurus_cxg/graph_generator/graph_generator.html#pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator.visualize_rdf_graph">visualize_rdf_graph() (pandasaurus_cxg.graph_generator.graph_generator.GraphGenerator method)</a>
</li>
</ul></td>
</tr></table>



</div>
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