uabbds/nf_xenium_analysis repository overview

⁠nf_xpatial Docker images

This repository contains the Docker images to the nf_xpatial workflow available at: https://github.com/U-BDS/nf_xpatial⁠

⁠nf_xpatial overview

nf_xpatial is a best-practices bioinformatics pipeline written in Nextflow that can be used to perform tertiary analysis on 10x Xenium data. It uses the output directories produced by the Xenium Onboard Analysis (XOA) instrument as input and performs quality control, filtering, normalization, and clustering, and generates configurable figures that can be reviewed individually or in the final summary report.

Notably, for cases where the raw data no longer follows the Xenium Onboard Analysis outputs (e.g.: sample was re-segmented with a third parity tool) nf_xpatial also accepts Seurat objects as input (per sample Seurat object without any data processed).