SpaNorm: spatially-aware normalization for spatial transcriptomics data

doi:10.1186/s13059-025-03565-y

Return

SpaNorm: spatially-aware normalization for spatial transcriptomics data

2025-04-29

DOI：10.1186/s13059-025-03565-y

Original

Original request for help

Save

Abstract

En 中文

Normalization of spatial transcriptomics data is challenging due to spatial association between region-specific library size and biology. We develop SpaNorm, the first spatially-aware normalization method that concurrently models library size effects and the underlying biology, segregates these effects, and thereby removes library size effects without removing biological information. Using 27 tissue samples from 6 datasets spanning 4 technological platforms, SpaNorm outperforms commonly used single-cell normalization approaches while retaining spatial domain information and detecting spatially variable genes. SpaNorm is versatile and works equally well for multicellular and subcellular spatial transcriptomics data with relatively robust performance under different segmentation methods.

Keywords:

SINGLE-CELL

ATLAS

Journal

Genome Biology

IF:

9.4

Papers:

6.4K

Citations:

7.3W

Organization

Univ Sydney

Scholars:

2.7K

Papers: 1.8K

Citations: 583

childrens med res inst

Scholars:

Papers: 9

Citations: 3

Walter and Eliza Hall Institute of Medical Research

Scholars:

671

Papers: 212

Citations: 1.0W

View more organizations

Cited Papers

High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis

NATURE COMMUNICATIONS

IF15.7

2023-12-19

OAAI

Janesick, Amanda; Shelansky, Robert; Gottscho, Andrew D.; Wagner, Florian; Williams, Stephen R.; Rouault, Morgane; Beliakoff, Ghezal; Morrison, Carolyn A.; Oliveira, Michelli F.; Sicherman, Jordan T.; Kohlway, Andrew; Abousoud, Jawad; Drennon, Tingsheng Yu; Mohabbat, Seayar H.; Taylor, Sarah E. B.

Save

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Nature Neuroscience

IF0

2021-02-08

OAAI

Kristen R. Maynard; Leonardo Collado-Torres; Lukas M. Weber; Cedric Uytingco; Brianna K. Barry; Stephen R. Williams; Joseph L. Catallini; Matthew N. Tran; Zachary Besich; Madhavi Tippani; Jennifer Chew; Yifeng Yin; Joel E. Kleinman; Thomas M. Hyde; Nikhil Rao; Stephanie C. Hicks; Keri Martinowich; Andrew E. Jaffe

Save

HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets

NUCLEIC ACIDS RESEARCH

IF13.1

2020-07-14

127

OAAI

Hounkpe, Bidossessi Wilfried; Chenou, Francine; de Lima, Franciele; De Paula, Erich Vinicius

Save

Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities

GENOME RESEARCH

IF5.5

2021-05-25

OAAI

Miller, Brendan F.; Bambah-Mukku, Dhananjay; Dulac, Catherine; Zhuang, Xiaowei; Fan, Jean

Save

A single-cell and spatially resolved atlas of human breast cancers

NATURE GENETICS

IF31.8

2021-09-06

628

OAAI

Wu, Sunny Z.; Al-Eryani, Ghamdan; Roden, Daniel Lee; Junankar, Simon; Harvey, Kate; Andersson, Alma; Thennavan, Aatish; Wang, Chenfei; Torpy, James R.; Bartonicek, Nenad; Wang, Taopeng; Larsson, Ludvig; Kaczorowski, Dominik; Weisenfeld, Neil, I; Uytingco, Cedric R.; Chew, Jennifer G.; Bent, Zachary W.; Chan, Chia-Ling; Gnanasambandapillai, Vikkitharan; Dutertre, Charles-Antoine; Gluch, Laurence; Hui, Mun N.; Beith, Jane; Parker, Andrew; Robbins, Elizabeth; Segara, Davendra; Cooper, Caroline; Mak, Cindy; Chan, Belinda; Warrier, Sanjay; Ginhoux, Florent; Millar, Ewan; Powell, Joseph E.; Williams, Stephen R.; Liu, X. Shirley; O'Toole, Sandra; Lim, Elgene; Lundeberg, Joakim; Perou, Charles M.; Swarbrick, Alexander

Save

The igraph software package for complex network research

IF0

PREAI

Save

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts

GENOME BIOLOGY

IF9.4

2016-04-27

789

OAAI

Lun, Aaron T. L.; Bach, Karsten; Marioni, John C.