This repo contains a scRNA-seq data processing pipeline and scripts for analysis for transcriptome resampling libraries. RMarkdown documents are provided to produce figures from the following publication.

Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries. Kent A Riemondy, Monica Ransom, Christopher Alderman, Austin E Gillen, Rui Fu, Jessica Finlay-Schultz, Gregory D Kirkpatrick, Jorge Di Paola, Peter Kabos, Carol A Sartorius, Jay R Hesselberth; Nucleic Acids Research, gky1204, https://doi.org/10.1093/nar/gky1204

snakemake pipeline for processing scRNA-seq fastqs to count matrices, assembling TCR seqs, and producing UMI summary flat files.

This directory contains a few utility R scripts. The globals.R file sets up constant variables and loads commonly used packages.

Collection of RMarkdown documents for producing figures. A snakemake pipeline is provided in the notebook subdirectory which runs the rmarkdowns in the correct order.

The snakemake data processing pipeline uses some C programs to perform fastq and bam processing steps. These are not necessary to run the analysis code. To compile these programs (requires C 11 compatible compiler, tested on linux and macOS):

cd bin
make