Scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data.

ABSTRACT:

Background

Single-cell RNA sequencing (scRNA-seq) enables the high-throughput quantification of transcriptional profiles in single cells. In contrast to bulk RNA-seq, additional preprocessing steps such as cell barcode identification or unique molecular identifier (UMI) deconvolution are necessary for preprocessing of data from single cell protocols. R packages that can easily preprocess data and rapidly visualize quality metrics and read alignments for individual cells across multiple samples or runs are still lacking.

Results

Here we present scruff, an R/Bioconductor package that preprocesses data generated from the CEL-Seq or CEL-Seq2 protocols and reports comprehensive data quality metrics and visualizations. scruff rapidly demultiplexes, aligns, and counts the reads map

SUBMITTER: Wang Z 

PROVIDER: S-EPMC6498700 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature