README.md

IRIS

Overview

This repository accompanies the manuscript disclosing the technology platform for integrated robotic imaging and sequencing (IRIS).

• IRIS provides paired image <> transcriptome per cell to perform phenomic studies.
• The manuscript (Bues, Pezoldt, Lambert, et al.) is accessible on biorxiv.
• The Fastq and processed sequencing data for scRNA-seq is available at:
  GEO: GSE300918

---

Structure

The repository contains:

• Pre-processing and QC pipeline for IRIS-derived scRNA-seq data

  • scRNAseq preprocessing

• Analysis and visualization code for sections in the manuscript:

  • Benchmarking (Figure 2 & 3)
  • Cell cycle (Figure 4 & 5)
  • T cells (Figure 6)

• Miscallaneous(./X_docs) includes envs, barcodes, functions, expression signatures and illustrations