{"repo":"nf-core/sopa","free":true,"listed":false,"github":"https://github.com/nf-core/sopa","clone":"git clone https://github.com/nf-core/sopa.git","description":"Nextflow version of Sopa - spatial omics pipeline and analysis","language":"Nextflow","stars":19,"topics":["pipeline","segmentation","spatial-omics","spatial-proteomics","spatial-transcriptomics","spatialdata","nextflow","nf-core","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/sopa is the Nextflow version of Sopa. Built on top of SpatialData, Sopa enables processing and analyses of spatial omics data with single-cell resolution (spatial transcriptomics or multiplex imaging data) using a standard data structure and output. We currently support the following technologies: Xenium, Visium HD, MERSCOPE, CosMX, PhenoCycler, MACSima, Molecural Cartography, and others. It outputs a .zarr directory containing a processed SpatialData object, and a .explorer directory for visualization. [!WARNING] If you are interested in the main Sopa python package, refer to this Sopa repository. Else, if you want to use Nextflow, you are in the good place. 1. (Visium HD only) Raw data processing with Space Ranger 2. (Optional) Tissue segmentation 3. Cell segmentation with Cellpose, Baysor, Proseg, Comseg, Stardist, ... 4. Aggregation, i.e. counting the transcripts inside the cells and/or averaging the channel intensities inside cells 5. (Optional) Cell-type annotation 6. User-friendly output creation for visualization and quick analysis 7. Full SpatialData object export as a .zarr directory After running nf-core/sopa , you can continue analyzing your SpatialData object with sopa as a Python package. Usage [!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. First, prepare a samplesheet that lists the data path to e","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/sopa/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}