{"repo":"nf-core/spatialaxe","free":true,"listed":false,"github":"https://github.com/nf-core/spatialaxe","clone":"git clone https://github.com/nf-core/spatialaxe.git","description":"A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data","language":"Python","stars":45,"topics":["nextflow","nf-core","pipeline","workflow","10x-genomics","image-processing","spatial","spatial-data-analysis","spatial-transcriptomics","transcriptomics"],"license":"MIT","category":"media-processing","readme_excerpt":"Introduction nf-core/spatialaxe is a bioinformatics best-practice processing and quality control pipeline for Xenium (and soon Atera) data. The current plan for the pipeline implementation is shown in the metromap below. The pipeline is under active developement and changes might occure frequently . [!NOTE] We are currently extending the pipeline for the 10x Atera system. Tools supported The pipeline supports the following tools: - Segmenation methods: - Baysor - Cellpose - Xenium ranger (XR) - StarDist - Segmentation free methods: - Ficture - Baysor - Transcript assignment methods: - Segger - Proseg - Utility methods: - SpatialData - Baysor - QC methods: - MultiQC Xenium Extra Plugin - OPT Usage On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website. [!NOTE] The pipeline does not support conda currently. We are working on it. Quick Start samplesheet.csv : Now, you can run the pipeline using: Run image-based segmentation mode CELLPOSE - BAYSOR - XR-IMPORT SEGMENTATION - SPATIALDATA - QC Run coordinate-based segmentation mode PROSEG - PROSEG2BAYSOR - XR-IMPORT SEGMENTATION - SPATIALDATA - QC Run s","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/spatialaxe/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."}