This repository contains KNIME workflows and R-code required for ‘pheno-seq’. pheno-seq is a method for combined imaging and gene expression profiling of single cell derived spheroids from three-dimensional cell culture systems to understand functional tumor cell heterogeneity. The pheno-seq manuscript is available as pre-print:
The methodology is based on the TakaraBio iCELL8™ technology that uses an automated dispenser and barcoded nanowells and was initially developed for single cell genomics applications.
This repository contains:
- Detailed pheno-seq protocol for microscopy and image analysis
- KNIME image analysis workflow for automated processing of nanowell microscopy images (PhenoSeq_preprocessing_SP8.knwf)
- Shiny web app R code for interactive analysis and selection of spheroids for sequencing (PhenoSelect.R)
- Additional KNIME image analysis workflows for functional validation assays
- R code for pheno-seq RNA-seq analysis
An example image dataset for testing the KNIME pre-processing workflow (raw) and a folder with already processed images & additional files for the PhenoSelect shiny web app (processed) can be downloaded here.