The DSP Workflow addresses a growing need to streamline the analysis of Spatial Transcriptomics data produced from Digital Spatial Profiling Technology (NanoString). It can be run in a docker container, and for biologists, in user-friendly web-based interactive notebooks (NIDAP, Palantir Foundry). It is based on the Bioconductor vignette “Analyzing GeoMx-NGS RNA Expression Data with GeomxTools”.
It has been tested on several Whole Transcriptome Atlas (WTA) human and mouse datasets. The workflow can be summarized in these steps: 
Future development will include support for protein data and integration with single cell datasets.
The development environment is provided in the Dockerfile/ directory, there are two sets of files: 1. Conda_container/ : The container includes a conda environment: DSPWorkflow_NDIAP. 2. Plain_R_container/ : Then container includes a plain R environment.