{"repo":"nf-core/nanostring","free":true,"listed":false,"github":"https://github.com/nf-core/nanostring","clone":"git clone https://github.com/nf-core/nanostring.git","description":"An analysis pipeline for Nanostring nCounter expression data.","language":"Nextflow","stars":18,"topics":["nf-core","nextflow","workflow","pipeline","nanostring","nanostringnorm"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/nanostring is a bioinformatics pipeline that can be used to analyze NanoString data. The performed analysis steps include quality control and data normalization. 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! Pipeline summary 1. Quality control with NACHO ( NACHO ) 2. Perform normalization with NACHO 3. Create count tables with provided metadata 4. Present QC for NanoString data ( MultiQC ) Pipeline tubemap 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 with your input data that looks as follows: samplesheet.csv : Each row represents a RCC file with counts. Now, you can run the pipeline using: [!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/nanostring/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."}