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nw20 committed Feb 9, 2024
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127 changes: 93 additions & 34 deletions genindex.html
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Expand Up @@ -108,41 +108,100 @@ <h1 class="site-logo" id="site-title">MalariaGEN parasite data user guide</h1>
</i>
</label>
<ul>
<li class="toctree-l2 has-children">
<a class="reference internal" href="pf7/analysis_examples/popgen.html">
Population Structure and Selection in Pf7
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/igv-notebook.html">
Visualizing Genomic Regions of Pf7 Samples with IGV Plots
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/sample-summary-table.html">
Summarise Samples by Administrative Division
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/sample-collection-over-time.html">
Visualising sample collections over time
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/barplot-samples-by-country.html">
Barplot of Samples by Country
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/variant-summary-table.html">
Summarise Genetic Variants
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/global-sample-map.html">
Plot Global Map of Samples
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/drug-resistance-summary.html">
Drug Resistance Frequencies Across Pf7
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/chloroquine-resistance-map.html">
Plot Map of Chloroquine Resistance
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/summarise_hrp2_hrp3_deletions.html">
Summarise
<em>
hrp2
</em>
and
<em>
hrp3
</em>
Deletions
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/visualise_hrp2_hrp3_deletions.html">
Visualise
<em>
hrp2
</em>
and
<em>
hrp3
</em>
Deletions
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/csp-cterm-analysis.html">
Analyse csp C-Terminal Variation
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/PCoA.html">
Principal Coordinate Analysis
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/geographic-genetic-differentiation.html">
Geographic patterns of population differentiation and gene flow
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/neighbour-joining-tree-swga.html">
Neighbour Joining Tree for sWGA vs. gDNA
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/proportion-eba175.html">
Plot
<em>
eba175
</em>
C Allele Proportions
</a>
<input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
<label for="toctree-checkbox-2">
<i class="fas fa-chevron-down">
</i>
</label>
<ul>
<li class="toctree-l3">
<a class="reference internal" href="pf7/analysis_examples/PCoA.html">
Principal Coordinate Analysis
</a>
</li>
<li class="toctree-l3">
<a class="reference internal" href="pf7/analysis_examples/geographic-genetic-differentiation.html">
Geographic patterns of population differentiation and gene flow
</a>
</li>
<li class="toctree-l3">
<a class="reference internal" href="pf7/analysis_examples/neighbour-joining-tree-swga.html">
Neighbour Joining Tree for sWGA vs. gDNA
</a>
</li>
<li class="toctree-l3">
<a class="reference internal" href="pf7/analysis_examples/proportion-eba175.html">
Plot
<em>
eba175
</em>
C Allele Proportions
</a>
</li>
</ul>
</li>
</ul>
</li>
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149 changes: 108 additions & 41 deletions landing-page.html
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Expand Up @@ -116,41 +116,100 @@ <h1 class="site-logo" id="site-title">MalariaGEN parasite data user guide</h1>
</i>
</label>
<ul>
<li class="toctree-l2 has-children">
<a class="reference internal" href="pf7/analysis_examples/popgen.html">
Population Structure and Selection in Pf7
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/igv-notebook.html">
Visualizing Genomic Regions of Pf7 Samples with IGV Plots
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/sample-summary-table.html">
Summarise Samples by Administrative Division
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/sample-collection-over-time.html">
Visualising sample collections over time
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/barplot-samples-by-country.html">
Barplot of Samples by Country
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/variant-summary-table.html">
Summarise Genetic Variants
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/global-sample-map.html">
Plot Global Map of Samples
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/drug-resistance-summary.html">
Drug Resistance Frequencies Across Pf7
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/chloroquine-resistance-map.html">
Plot Map of Chloroquine Resistance
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/summarise_hrp2_hrp3_deletions.html">
Summarise
<em>
hrp2
</em>
and
<em>
hrp3
</em>
Deletions
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/visualise_hrp2_hrp3_deletions.html">
Visualise
<em>
hrp2
</em>
and
<em>
hrp3
</em>
Deletions
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/csp-cterm-analysis.html">
Analyse csp C-Terminal Variation
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/PCoA.html">
Principal Coordinate Analysis
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/geographic-genetic-differentiation.html">
Geographic patterns of population differentiation and gene flow
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/neighbour-joining-tree-swga.html">
Neighbour Joining Tree for sWGA vs. gDNA
</a>
</li>
<li class="toctree-l2">
<a class="reference internal" href="pf7/analysis_examples/proportion-eba175.html">
Plot
<em>
eba175
</em>
C Allele Proportions
</a>
<input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/>
<label for="toctree-checkbox-2">
<i class="fas fa-chevron-down">
</i>
</label>
<ul>
<li class="toctree-l3">
<a class="reference internal" href="pf7/analysis_examples/PCoA.html">
Principal Coordinate Analysis
</a>
</li>
<li class="toctree-l3">
<a class="reference internal" href="pf7/analysis_examples/geographic-genetic-differentiation.html">
Geographic patterns of population differentiation and gene flow
</a>
</li>
<li class="toctree-l3">
<a class="reference internal" href="pf7/analysis_examples/neighbour-joining-tree-swga.html">
Neighbour Joining Tree for sWGA vs. gDNA
</a>
</li>
<li class="toctree-l3">
<a class="reference internal" href="pf7/analysis_examples/proportion-eba175.html">
Plot
<em>
eba175
</em>
C Allele Proportions
</a>
</li>
</ul>
</li>
</ul>
</li>
Expand Down Expand Up @@ -284,13 +343,21 @@ <h1>MalariaGEN parasite data user guide<a class="headerlink" href="#malariagen-p
<ul>
<li class="toctree-l1"><a class="reference internal" href="pf7/Data_access.html">Pf7 Data Access</a></li>
<li class="toctree-l1"><a class="reference internal" href="pf7/examples.html">Pf7 Analysis Examples</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/popgen.html">Population Structure and Selection in Pf7</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pf7/analysis_examples/PCoA.html">Principal Coordinate Analysis</a></li>
<li class="toctree-l3"><a class="reference internal" href="pf7/analysis_examples/geographic-genetic-differentiation.html">Geographic patterns of population differentiation and gene flow</a></li>
<li class="toctree-l3"><a class="reference internal" href="pf7/analysis_examples/neighbour-joining-tree-swga.html">Neighbour Joining Tree for sWGA vs. gDNA</a></li>
<li class="toctree-l3"><a class="reference internal" href="pf7/analysis_examples/proportion-eba175.html">Plot <em>eba175</em> C Allele Proportions</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/igv-notebook.html">Visualizing Genomic Regions of Pf7 Samples with IGV Plots</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/sample-summary-table.html">Summarise Samples by Administrative Division</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/sample-collection-over-time.html">Visualising sample collections over time</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/barplot-samples-by-country.html">Barplot of Samples by Country</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/variant-summary-table.html">Summarise Genetic Variants</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/global-sample-map.html">Plot Global Map of Samples</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/drug-resistance-summary.html">Drug Resistance Frequencies Across Pf7</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/chloroquine-resistance-map.html">Plot Map of Chloroquine Resistance</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/summarise_hrp2_hrp3_deletions.html">Summarise <em>hrp2</em> and <em>hrp3</em> Deletions</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/visualise_hrp2_hrp3_deletions.html">Visualise <em>hrp2</em> and <em>hrp3</em> Deletions</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/csp-cterm-analysis.html">Analyse csp C-Terminal Variation</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/PCoA.html">Principal Coordinate Analysis</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/geographic-genetic-differentiation.html">Geographic patterns of population differentiation and gene flow</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/neighbour-joining-tree-swga.html">Neighbour Joining Tree for sWGA vs. gDNA</a></li>
<li class="toctree-l2"><a class="reference internal" href="pf7/analysis_examples/proportion-eba175.html">Plot <em>eba175</em> C Allele Proportions</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pf7/api.html">Pf7 API</a></li>
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