This repository contains the code for the data analysis performed in the manuscript “RNA-based cell hashing enables sample multiplexing without dedicated barcode capture”.
This repository contains the analysis of Smart-seq3xpress (SS3x) and 10x chromium (droplet_scRNAseq) data sets of sbRNA-labelled cell lines, and the analyses for comparison of cell detachment methods, viability assay, and lectin stainings (detachment_viability_staining). The code files produce the numbers and figures presented in the manuscript.
The analyses and files required to reproduce the figures of the manuscript are organized in individual sub-directories. These contain .Rproj and .Rmd files among other files used in the analyses, and the generic sbRNA FASTA reference for the 10x experiment.
The analysis was done in R (version 4.4.2) and RStudio Server (version 2023.12.1). Packages including versions used for the analyses are recorded using renv (version 1.0.11).
The datasets (e.g. sequencing FASTQ files and count matrices) generated for this manuscript are available on ArrayExpress under accession numbers E-MTAB-17623 (SS3x) and E-MTAB-17624 (10x).