https://github.com/fertiglab/spatial-pipeline

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Last synced: 8 months ago · JSON representation

Repository

Created over 2 years ago · Last pushed over 1 year ago

Readme

Run CoGAPS followed by SpaceMarkers to find spatially interacting genes in Visium data.

Locally with docker installed (see samplesheet.csv for reference):

nextflow run FertigLab/spatial-pipeline --input [samplesheet] -w [workdir] -profile docker -r main

Other running options - check out profiles in nextflow.config.

[!TIP] Use --max_memory --max_cpus --max_time to control the maximum resources to grant on the host.

Software projects in computational biology and bioinformatics in Elana Fertig's lab in Oncology Biostatistics and Bioinformatics at JHMI