Package: scruff
Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Version: 1.28.0
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: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:46:27 UTC
RemoteUrl: https://github.com/bioc/scruff
RemoteRef: RELEASE_3_22
RemoteSha: 085152e45bb96cf7932a4f853637869aa435971d
NeedsCompilation: no
Packaged: 2026-01-23 07:30:51 UTC; root
Author: Zhe Wang [aut, cre],
  Junming Hu [aut],
  Joshua Campbell [aut]
Maintainer: Zhe Wang <zhe@bu.edu>
Built: R 4.5.2; ; 2026-01-23 07:33:35 UTC; windows
