nf-core/spaceranger_count

module

Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data

align count spatial spaceranger imaging

Module Information

Repository: https://github.com/nf-core/modules/tree/master/modules/nf-core/spaceranger/count
Source: nf-core
Organization: nf-core
Authors: @grst
Maintainers: @grst , @fasterius

Tools

spaceranger

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.

License: 10x Genomics EULA

Inputs

Name	Type	Description
0
reference	directory	Folder containing all the reference indices needed by Space Ranger
probeset	file	OPTIONAL - Probe set specification.

Quick Start

Include this module in your Nextflow pipeline:

include { SPACERANGER_COUNT } from 'https://github.com/nf-core/modules/tree/master/modules/nf-core/spaceranger/count'

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