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 ./Install_containers.sh
Add all need paramters in the csvParams.config
Load nextflow module ml Nextflow/23.04.2
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 22 Commits
Spatial_barcodes		Spatial_barcodes
bin		bin
modules		modules
testing		testing
.DS_Store		.DS_Store
ERV_barcodes		ERV_barcodes
Install_containers.sh		Install_containers.sh
NF_Elena.config		NF_Elena.config
NF_Elena.nf		NF_Elena.nf
Old_Conf.config		Old_Conf.config
Old_Params.config		Old_Params.config
Old_pipeline.nf		Old_pipeline.nf
QSP_likePipeline.nf		QSP_likePipeline.nf
README.md		README.md
ST_analysis.nf		ST_analysis.nf
csvParams.config		csvParams.config
nextflow.config		nextflow.config
paramsElena.config		paramsElena.config
test.config		test.config
testR.nf		testR.nf