Data export

This chapter describes only Exporters functionality specific to the CLC Single Cell Analysis Module.

Exporters exist for exporting Expression Matrix (Image expression_matrix_track_16_n_p) / (Image expr_matrix_spliced_unspliced_16_n_p) to the following formats:

Note: While it is possible to export normalized expression values, this is only provided for interoperability with other software. If such values are re-imported, the resulting Expression Matrix may not work as intended in tools that assume values look like counts (such as Normalize Single Cell Data) or are equal to or larger than zero (such as Predict Cell Types). For this reason, when sharing data with other users of CLC Single Cell Analysis Module, it is recommended to export in CLC format. This preserves both the raw expression values and the normalized values.

Additionally, exporters exist for exporting a Peak Count Matrix (Image peak_count_matrix_16_n_p) to Cell Ranger HDF5 and MEX.

To launch the export toolbox use the menu or click the Export button in the top left corner of the Workbench. To export an expression or peak matrix, start typing "matrix" to get to the selection, see figure 3.1.

Image exporters
Figure 3.1: Exporters available for exporting single cell expression matrices



Subsections