scruff
This is the development version of scruff; for the stable release version, see scruff.
All Bioconductor versions of scruff
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Bioconductor version: 3.24 · Package version: 1.31.0
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 bu.edu>
Citation
From within R, enter citation("scruff"):
Zhe Wang, Junming Hu, Joshua Campbell. scruff: Single Cell RNA-Seq UMI Filtering Facilitator (scruff). doi:10.18129/B9.bioc.scruff, R package version 1.31.0, https://bioconductor.org/packages/scruff.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scruff")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.31.0 |
| License | MIT + file LICENSE |
| Bug Reports | https://github.com/campbio/scruff/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| Downloads rank | 805 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Technology, Visualization, WorkflowStep |
| Package Short Url | https://bioconductor.org/packages/scruff/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scruff")| Process scRNA-Seq reads in scruff | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | scruff_1.31.0.tar.gz |
| Windows binary (x86_64) | scruff_1.31.0.zip |
| macOS binary (arm64) | scruff_1.31.0.tgz |
| macOS binary (x86_64) | scruff_1.31.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scruff |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scruff |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.0)
Imports: data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly, patchwork