About

SpaGFT is a python package to analyze tissue functions empowered using spatial omcis data.

Given the raw count matrix of spatial transcriptomics data and corresponding spatial coordinate information, SpaGFT transforms grapg gene expression to frequency domain (also called spectral domain), i.e., finding a new topological feature representation method of genes which combined gene expression and spatial information of spots simultaneously. SpaGFT can transform complex spatial patterns into one-dimensional, simple but informative Fourier Coefficients (FCs). In this way, several tasks can be achieved by analyzing FCs, include identifying spatially variable genes (SVG), and enhancing gene expression.

SpaGFT’s functions

  • Transform gene expression to FCs.

  • Identify spatially variable features, including but not limited to genes and proteins.

  • Enhance spatial signals (e.g., gene expression).

SpaGFT’s advantages

  • Hypothesis-free. SpaGFT is a hypothesis-free graph Fourier transform framework (GFT) from spatial transcriptomics data without assuming any spatial distribution patterns.

  • Computational effectiveness and efficiency. SpaGFT can run on PC directly and still keep high accuracy and efficiency (time complexity is O(n^2)).

  • SpaGFT can be also used for sequencing-based and imaging-based spatial transcriptomics, spatial-CITE-seq, and spatial proteomics.