DOI: 10.18129/B9.bioc.scruff    

This is the development version of scruff; for the stable release version, see scruff.

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Bioconductor version: Development (3.17)

A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.

Author: Zhe Wang [aut, cre], Junming Hu [aut], Joshua Campbell [aut]

Maintainer: Zhe Wang <zhe at>

Citation (from within R, enter citation("scruff")):


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HTML R Script Process Single Cell RNA-Seq reads using scruff
PDF   Reference Manual


biocViews Alignment, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Technology, Visualization, WorkflowStep
Version 1.17.0
In Bioconductor since BioC 3.8 (R-3.5) (4 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports data.table, GenomicAlignments, GenomicFeatures, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread
Suggests BiocStyle, knitr, rmarkdown, testthat
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