{"repo":"nf-core/spatialvi","free":true,"listed":false,"github":"https://github.com/nf-core/spatialvi","clone":"git clone https://github.com/nf-core/spatialvi.git","description":"Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.","language":"Nextflow","stars":81,"topics":["nf-core","nextflow","workflow","pipeline","10x-genomics","10xgenomics","bioinformatics","image-processing","microscopy","rna-seq"],"license":"MIT","category":"media-processing","readme_excerpt":"Introduction nf-core/spatialvi is a bioinformatics analysis pipeline for Visium spatial transcriptomics data from 10x Genomics. It can process and analyse spatial data either directly from raw data by running Space Ranger or data already processed by Space Ranger. The pipeline currently consists of the following steps: The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! 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. 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","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/spatialvi/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."}