DESCRIPTION

Package: scruff
Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Version: 1.3.6
Date: 2019-08-08
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 (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
RoxygenNote: 6.1.1
VignetteBuilder: knitr
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
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    Rsubread,
    testthat
biocViews:
    Software,
    Technology,
    Sequencing,
    Alignment,
    RNASeq,
    SingleCell,
    WorkflowStep,
    Preprocessing,
    QualityControl,
    Visualization,
    ImmunoOncology
BugReports: https://github.com/campbio/scruff/issues