This repository contains the data and scripts associated with the paper:

"A comprehensive workflow for allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data"

Authors: Ahmad Al Ajami, Jonas Schuck, Federico Marini, Katharina Imkeller.

Input data and Rds intermediate files are uploaded to Zenodo: https://doi.org/10.5281/zenodo.14033960.

Code, data, and intermediate files are used to generate the figures in the paper.

Please cite the paper if you use this data or workflow in your research.

Data analysis was performed on:

• R version 4.4.1 (2024-06-14)
• Platform: x86_64-pc-linux-gnu
• Running under: Ubuntu 20.04.6 LTS

The R packages/software used:

• tidyverse (Wickham et al., 2019)
• SingleCellExperiment (Amezquita et al., 2020)
• scran (Lun et al., 2016)
• scater (McCarthy et al., 2017)
• igraph (Csardi & Nepusz, 2006)
• bluster (Lun, 2022)
• ggplot2 (Wickham, 2016)
• pheatmap (Kolde, 2019)
• patchwork (Pedersen, 2022)
• cowplot (Wilke, 2020)
• scDblFinder (Germain et al., 2021)
• gridExtra (Auguie & Antonov, 2017)
• DropletUtils (Lun et al., 2019)
• BiocParallel (Morgan et al., 2024)
• Matrix (Bates et al., 2024)
• AnnotationHub (Morgan & Shepherd, 2024)
• batchelor (Haghverdi et al., 2018)
• RColorBrewer (Neuwirth, 2022)
• immunotation (Imkeller, 2024)
• reshape2 (Wickham, 2007)
• scales (Wickham et al., 2023)
• Biostrings (Pagès et al., 2024)
• readr (Wickham et al., 2024)