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.

Updates (Feb 20, 2025)

If you are working with large image-based spatial data, such as Xenium 5k samples, and encounter a warning from the SpatialExperiment class when storing molecule detections, please set use_cm=TRUE and run jazzPanda using the count matrix and cell coordinates to avoid integer overflow issues.

We are actively updating the structure to better support large-scale transcript detection data.

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")