NicheDECODE workflow for inference of spatial niche abundances from tissue-level omics data v2

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.

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Publication Details

Published
2026-10-30
DOI
https://doi.org/10.17504/protocols.io.6wgq9rq2xlk5/v2
Primary Topic
Single-cell and spatial transcriptomics
Type
preprint
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preprint

NicheDECODE workflow for inference of spatial niche abundances from tissue-level omics data v2

Renjie Liu
6 links
Single-cell and spatial transcriptomics
preprint

NicheDECODE workflow for inference of spatial niche abundances from tissue-level omics data v2

Renjie Liu
preprint en

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.

Harbin Institute of Technology (CN)
Single-cell and spatial transcriptomics
DOIOpen Access PDFOpenAlex
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NicheDECODE workflow for inference of spatial niche abundances from tissue-level omics data v2 — Renjie Liu · (2026) | TGRS Research Map | TGRS