Package: scruff Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff) Version: 1.31.0 Date: 2024-03-27 Authors@R: c(person("Zhe", "Wang", email = "zhe@bu.edu", role = c("aut", "cre")), person("Junming", "Hu", email = "hjunming@bu.edu", role = c("aut")), person("Joshua", "Campbell", email = "camp@bu.edu", role = c("aut"))) Description: 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. Depends: R (>= 4.0) License: MIT + file LICENSE Encoding: UTF-8 LazyData: TRUE RoxygenNote: 7.3.3 VignetteBuilder: knitr 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 Suggests: BiocStyle, knitr, rmarkdown, testthat biocViews: Software, Technology, Sequencing, Alignment, RNASeq, SingleCell, WorkflowStep, Preprocessing, QualityControl, Visualization, ImmunoOncology BugReports: https://github.com/campbio/scruff/issues Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:48:20 UTC RemoteUrl: https://github.com/bioc/scruff RemoteRef: HEAD RemoteSha: 3278f3a17acd28c0fa934aa354dacf234e589a35 NeedsCompilation: no Packaged: 2026-07-05 14:01:35 UTC; root Author: Zhe Wang [aut, cre], Junming Hu [aut], Joshua Campbell [aut] Maintainer: Zhe Wang