Singular Genomics Docs
These pages provide documentation, example workflows, and helper tools for analyzing, and post-processing data generated by the G4X spatial sequencer.
G4X-helpers
Post-processing tools and helper models 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 its CLI features
G4X-viewer
Explore and visualize your G4X-data
The G4X-viewer is a Python-based, multi-purpose, interactive viewer specifically designed to help you explore your G4X-data. The G4X-viewer is accessible through our website or can be downloaded from GitHub as a standalone application and hosted locally.
In this section, you can:
- find resources to learn how to navigate your data with the G4X-viewer
G4X-data
Reference documentation for G4X-output files
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
G4X-tutorials
Get started analyzing your data
G4X Tutorials are a collection of example workflows that demonstrate how to analyze G4X-data using popular Python and R libraries. These tutorials cover a wide range of topics, from basic data import and visualization to advanced analysis techniques.
In this section, you can:
- learn how to plot spatial tissue information from the G4X-data
- generate novel nuclear or cytoplasmic segmentations with popular models
Support
Got feedback or ideas for additional tutorials or documentation?
drop us a note at care@singulargenomics.com.
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