GeneSurfer is an interactive interface for exploring localized transcriptome-wide gene co-expression patterns in the 3D spatial domain.
This software is described in GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data.
GeneSurfer is built as a plug-in for the ManiVault application building system. For more information about ManiVault Studio, see ManiVault.
The installer of this software which includes the GeneSurfer plugin can be downloaded here.
Currently, only a Windows installer is provided, Linux and Mac will follow in the coming period.
The Allen Brain Cell Atlas dataset is used to demonstrate the usage of GeneSurfer. To explore this dataset, a minimum of 16GB of memory is required. Download the project file containing this dataset here.
Yao, Z., van Velthoven, C.T.J., Kunst, M. et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 624, 317–332 (2023). https://doi.org/10.1038/s41586-023-06812-z