G4X-tutorials
Welcome to G4X-tutorials.
These pages provide documentation, example workflows, and helper tools for analyzing, and post-processing data generated by the G4X spatial sequencer.
G4X-helpers
Helper models and post-processing tools for G4X data.
With G4X-helpers we provide an open-source toolkit for common post-processing tasks — such as applying custom segmentations or adding your own labels to the G4X-viewer. You can access its core features from the command-line interface (CLI) and additionally import it as a standalone Python package to interact with your data.
In this section you can:
- learn how to install G4X-helpers on your system
- get started with using the command line interface (CLI)
- find a description of CLI features
G4X data
Output reference and analysis import guides.
The G4X produces multi-modal output containing tables, images, arrays and annotated matrices for single-cell analysis.
The files found in the output directory are compatible with popular Python libraries from the scverse ecosystem, like scanpy, rapids-singlecell, squidpy, and spatial-data and, if you prefer working in R, can be easily imported into Seurat.
In this section you will find:
- details on the G4X output files and their organization
- guides on importing G4X data into popular analysis tools in Python and R
support
Got feedback or ideas for additional tutorials?
drop us a note at care@singulargenomics.com.
Found a bug or want to report another problem regarding G4X-helpers?
please file a new issue on the G4X-helpers issue tracker
Want to get involved and add new features?
check out how to contribute
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