Deploy preview for PR 51 🛫

pr-preview/pr-51/components/modules/annotate/popv.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/annotate/popv" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/annotate/popv" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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 </div></div><p>Note that this is a one-shot version of PopV.</p>
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pr-preview/pr-51/components/modules/cluster/leiden.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/cluster/leiden" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/cluster/leiden" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
 </section>
 </div></div><p>Leiden is an improved version of the Louvain algorithm [Blondel08]. It has been proposed for single-cell analysis by [Levine15]. This requires having ran <code>neighbors/find_neighbors</code> or <code>neighbors/bbknn</code> first.</p>
 <p>Blondel08: Blondel et al.&nbsp;(2008), Fast unfolding of communities in large networks, J. Stat. Mech.<br>

pr-preview/pr-51/components/modules/compression/compress_h5mu.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/compression/compress_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/compression/compress_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/convert/from_10xh5_to_h5mu.html

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+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_10xh5_to_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/convert/from_10xmtx_to_h5mu.html

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+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_10xmtx_to_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/convert/from_bd_to_10x_molecular_barcode_tags.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/convert/from_bd_to_10x_molecular_barcode_tags" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_bd_to_10x_molecular_barcode_tags" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/convert/from_bdrhap_to_h5mu.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/convert/from_bdrhap_to_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_bdrhap_to_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/convert/from_cellranger_multi_to_h5mu.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/convert/from_cellranger_multi_to_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_cellranger_multi_to_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
 </section>
 </div></div><p>By default, will map the following library type names to modality names: - Gene Expression: rna - Peaks: atac - Antibody Capture: prot - VDJ: vdj - VDJ-T: vdj_t - VDJ-B: vdj_b - CRISPR Guide Capture: crispr - Multiplexing Capture: hashing</p>
 <p>Other library types have their whitepace removed and dashes replaced by underscores to generate the modality name.</p>

pr-preview/pr-51/components/modules/convert/from_h5ad_to_h5mu.html

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+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_h5ad_to_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/convert/from_h5mu_to_h5ad.html

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+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_h5mu_to_h5ad" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/convert/velocyto_to_h5mu.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/velocity/velocyto_to_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/velocity/velocyto_to_h5mu" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
 </section>
 </div></div><p>If an input h5mu file is also provided, the velocity h5ad object will get added to that h5mu instead.</p>
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pr-preview/pr-51/components/modules/correction/cellbender_remove_background.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/correction/cellbender_remove_background" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/correction/cellbender_remove_background" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
 </section>
 </div></div><p>This module removes counts due to ambient RNA molecules and random barcode swapping from (raw) UMI-based scRNA-seq count matrices. At the moment, only the count matrices produced by the CellRanger count pipeline is supported. Support for additional tools and protocols will be added in the future. A quick start tutorial can be found here.</p>
 <p>Fleming et al.&nbsp;2022, bioRxiv.</p>

pr-preview/pr-51/components/modules/correction/cellbender_remove_background_v0_2.html

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+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/correction/cellbender_remove_background_v0_2" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
 </section>
 </div></div><p>This module removes counts due to ambient RNA molecules and random barcode swapping from (raw) UMI-based scRNA-seq count matrices. At the moment, only the count matrices produced by the CellRanger count pipeline is supported. Support for additional tools and protocols will be added in the future. A quick start tutorial can be found here.</p>
 <p>Fleming et al.&nbsp;2022, bioRxiv.</p>

pr-preview/pr-51/components/modules/dataflow/concat.html

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+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/dataflow/concat" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/dataflow/merge.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/dataflow/merge" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/dataflow/merge" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/dataflow/split_modalities.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/dataflow/split_modalities" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/dataflow/split_modalities" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/demux/bcl2fastq.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/demux/bcl2fastq" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/demux/bcl2fastq" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/demux/bcl_convert.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/demux/bcl_convert" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/demux/bcl_convert" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
 </section>
 </div></div><p>Information about upgrading from bcl2fastq via https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html and https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html</p>
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pr-preview/pr-51/components/modules/demux/cellranger_mkfastq.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/demux/cellranger_mkfastq" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/demux/cellranger_mkfastq" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/dimred/pca.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/dimred/pca" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/dimred/pca" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
 </section>
 </div></div><p>Uses the implementation of scikit-learn [Pedregosa11]</p>
 <section id="example-commands" class="level2">

pr-preview/pr-51/components/modules/dimred/umap.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/dimred/umap" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/dimred/umap" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
 </section>
 </div></div><p>Besides tending to be faster than tSNE, it optimizes the embedding such that it best reflects the topology of the data, which we represent throughout Scanpy using a neighborhood graph. tSNE, by contrast, optimizes the distribution of nearest-neighbor distances in the embedding such that these best match the distribution of distances in the high-dimensional space. We use the implementation of umap-learn [McInnes18]. For a few comparisons of UMAP with tSNE, see this preprint</p>
 <section id="example-commands" class="level2">

pr-preview/pr-51/components/modules/download/download_file.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/download/download_file" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/download/download_file" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/download/sync_test_resources.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/download/sync_test_resources" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/download/sync_test_resources" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/files/make_params.html

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+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/files/make_params" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/filter/do_filter.html

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+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/filter/do_filter" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
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pr-preview/pr-51/components/modules/filter/filter_with_counts.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/filter/filter_with_counts" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/filter/filter_with_counts" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
 </section>
 </div></div><p>This is based on both the UMI counts, the gene counts and the mitochondrial genes (genes starting with mt/MT)</p>
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pr-preview/pr-51/components/modules/filter/filter_with_hvg.html

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-<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/./src/filter/filter_with_hvg" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
+<p><a href="https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/filter/filter_with_hvg" class="btn-action btn-sm btn-info btn" role="button">Source</a></p>
 </section>
 </div></div><p>Expects logarithmized data, except when flavor=‘seurat_v3’ in which count data is expected.</p>
 <p>Depending on flavor, this reproduces the R-implementations of Seurat [Satija15], Cell Ranger [Zheng17], and Seurat v3 [Stuart19].</p>