Finding spatially relevant marker genes in image based spatial transcriptomics data • jazzPanda

jazzPanda: A hybrid approach to find spatially relevant marker genes

in image-based spatial transcriptomics data

Introduction

The jazzPanda package contains functions to find marker genes based on the spatial coordinates for imaging-based spatial transcriptomics technologies including 10x Xenium, NanoString CosMx and Vizgen MERSCOPE.

Installation

To install jazzPanda from Bioconductor, use the following commands:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("jazzPanda")

To install jazzPanda from github, use the following commands:

library(devtools)
devtools::install_github("phipsonlab/jazzPanda")

In order to view the vignette for jazzPanda use the following command:

browseVignettes("jazzPanda")

Example analyses

Worked analyses applying jazzPanda to a range of imaging-based spatial transcriptomics datasets (10x Xenium, NanoString CosMx and Vizgen MERSCOPE) are available as a workflowr website:

Analysis website: https://phipsonlab.github.io/jazzPanda_workflowr/

Citation

If you use jazzPanda in your research, please cite our preprint:

Jin X, Putri GH, Cheng J, Asselin-Labat M-L, Smyth GK, Phipson B (2026). jazzPanda: spatially aware marker gene detection for imaging-based spatial transcriptomics. bioRxiv. doi: 10.64898/2026.02.13.705867