scruff

Scruff is an R package designed to streamline the preprocessing of data generated from single-cell RNA sequencing (scRNA-seq) protocols, specifically CEL-Seq or CEL-Seq2. Unlike bulk RNA-seq, scRNA-seq requires additional preprocessing steps such as cell barcode identification and unique molecular identifier (UMI) deconvolution. Scruff efficiently demultiplexes, aligns, and counts reads mapped to genome features while deduplicating UMIs. The package offers comprehensive data quality metrics and visualizations, including pre-and post-alignment metrics for cells across multiple experiments. It enables detailed visualization of read alignments with UMI information, highlighting differences in isoform usage. Scruff supports the visualization of quality metrics for sequence alignment files from Cell Ranger by 10X Genomics.