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 Export section, in addition to Download data link at the bottom of the Toolbox, provides means of exporting data from Partek Flow.

Export to h5ad files

Section headings should use level 2 heading, while the content of the section should use paragraph (which is the default). You can choose the style in the first dropdown in toolbarAn .h5ad files a .hdf5 file with some additional structure specifying how to store AnnData objects. The tool Export to h5ad files enables the user to export count matrix data from Partek Flow and add all the sample-level and cell-level attributes. 

Select a count matrix-type data node (e.g. Single cell counts, Filtered counts, Normalised counts, SC scaled data, Integrated counts, Classify result, Annotated counts) and the Export section will appear in the Toolbox. Expand it and select Export to h5ad files (Figure 1).

On the setup dialog, you can specify optional annotations to be added to the cells: PCA (coordinates), t-SNE (coordinates), UMAP (coordinates), and Graph-based cluster (cluster identifier) (Figure 2). If no optional annotation is selected, only the information present in the selected count matrix node will be included in the .h5ad file.

Clicking on a Select data node button opens up the pipeline preview (Figure 3). Partek Flow will highlight the data nodes with the same number of cells as the selected count matrix node, and information from one of those nodes can be added to the .h5ad file. Left-click on a node and click Select to confirm (or Cancel to close the preview).

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