Package: scruff 1.30.0

Zhe Wang

scruff: Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

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.

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

scruff_1.30.0.tar.gz
scruff_1.30.0.zip(r-4.7)scruff_1.30.0.zip(r-4.6)scruff_1.30.0.zip(r-4.5)
scruff_1.30.0.tgz(r-4.6-any)scruff_1.30.0.tgz(r-4.5-any)
scruff_1.30.0.tar.gz(r-4.7-any)scruff_1.30.0.tar.gz(r-4.6-any)
scruff_1.30.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scruff/json (API)
NEWS

# Install 'scruff' in R:

install.packages('scruff', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/campbio/scruff/issues

Datasets:

bamExample - Example GAlignments Object
barcodeExample - A vector of example cell barcodes.
cbtop10000 - Top 10,000 rows for v1, v2, and v3 cell barcode whitelist files
sceExample - Example SingleCellExperiment Object
validCb - Cell barcode whitelist

On BioConductor:scruff-1.31.0(bioc 3.24)scruff-1.30.0(bioc 3.23)

software technology sequencing alignment rnaseq singlecell workflowstep preprocessing qualitycontrol visualization immunooncology bioinformatics scrna-seq single-cell umi

6.44 score 10 stars 23 scripts 1 mentions 8 exports 158 dependencies

Last updated from:b8ea4f78da (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	235
linux-devel-x86_64	NOTE	523
source / vignettes	OK	402
linux-release-x86_64	NOTE	538
macos-release-arm64	NOTE	350
macos-oldrel-arm64	NOTE	246
windows-devel	NOTE	460
windows-release	NOTE	408
windows-oldrel	NOTE	404
wasm-release	OK	193

Exports:alignRsubread countUMI demultiplex gview qcplots rview scruff tenxBamqc

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes glue graph gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 hwriter interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nnet openssl OrganismDbi parallelly patchwork pillar pkgconfig plyr png prettyunits progress ProtGenerics purrr pwalign R6 rappdirs RBGL RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi Rsubread rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo ShortRead SingleCellExperiment snow SparseArray stringdist stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 XVector yaml

Process scRNA-Seq reads in scruff

Zhe Wang

Rendered fromscruff.Rmdusingknitr::rmarkdownon Jun 19 2026.

Last update: 2025-10-06
Started: 2017-11-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A wrapper to 'Rsubread' read alignment function 'align'	alignRsubread
Example GAlignments Object	bamExample
A vector of example cell barcodes.	barcodeExample
Top 10,000 rows for v1, v2, and v3 cell barcode whitelist files	cbtop10000
Count the number of UMIs for each gene and output count matrix	countUMI
Demultiplex cell barcodes and assign cell specific reads	demultiplex
Visualize gene isoforms	gview
Visualize data quality	qcplots
Visualize aligned reads	rview
Example SingleCellExperiment Object	sceExample
Run scruff pipeline	scruff
Generate and output 10X read alignment data quality metrics	tenxBamqc
Cell barcode whitelist (737K-august-2016.txt)	validCb