NicheDECODE workflow for inference of spatial niche abundances from tissue-level omics data v1
Year: 2026
Type: preprint
Abstract: This protocol describes the NicheDECODE workflow for estimating spatial niche abundances from tissue-level omics data using an annotated spatial reference. It covers environment setup, data preparation, pseudo-tissue generation, integration of spatial and functional features, model training, and niche-abundance prediction. Code, example notebooks and input data are provided through the accompanying GitHub repository and Zenodo archives.
Author: Renjie Liu
Institution: Harbin Institute of Technology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7224830351