Spatial Transcriptomics OncoRNA Lab

pipeline for the analysis of Spatial Transcriptomics data generated from our custom microarray

Requirements

clone the repository git clone https://github.com/francops1722/ST_transcriptomics.git
Download containers ./build_containers.sh
Add all need paramters in the csvParams.config
Load nextflow module ml Nextflow/24.10.2
Run pipeline nextflow run ST_analysis.nf -c nextflow.config -with-dag ST_flowchart.png

Name		Name	Last commit message	Last commit date
Latest commit History 30 Commits
Spatial_barcodes		Spatial_barcodes
bin		bin
modules		modules
subworkflows		subworkflows
test		test
workflows		workflows
.DS_Store		.DS_Store
.gitignore		.gitignore
Params.config		Params.config
README.md		README.md
STpipeline_job.pbs		STpipeline_job.pbs
build_containers.sh		build_containers.sh
main.nf		main.nf
nextflow.config		nextflow.config
nextflow_schema.json		nextflow_schema.json