DESCRIPTION

Package: DropletQC
Title: Calculate Nuclear Fraction Score
Version: 0.0.0.9000
Authors@R:
    person(given = "Walter",
           family = "Muskovic",
           role = c("aut", "cre"),
           email = "w.muskovic@gmail.com")
BugReports: https://powellgenomicslab.github.io/DropletQC/issues
Description: This simple R package can be used to calculate a useful QC metric 
    for single cell RNA-seq datasets generated with the 10x Genomics Chromium
    Single Cell Gene Expression platform: the nuclear fraction score. This score
    captures, for each input cell barcode, the fraction of RNA that likely 
    originated from unspliced (nuclear) pre-mRNA. Sheared cell membranes from 
    damaged cells in the input cell suspension primarily release cytoplasmic RNA
    into solution, while the nuclear envelope remains intact. As a result, RNA
    released from stressed or damaged cells consists mostly of mature 
    cytoplasmic mRNA and is relatively depleted of unspliced nuclear precursor 
    mRNA. This fact can be useful in identifying both; droplets containing only 
    ambient RNA, characterised by a low nuclear fraction score, and damaged 
    cells, which can be identified by a high score. The QC metric is calculated 
    by parsing the input barcoded BAM file for CB and RE flags added by 10x 
    Genomics' Cell Ranger software.
Maintainer: Walter Muskovic <w.muskovic@gmail.com>
License: MIT + file LICENSE
URL: https://powellgenomicslab.github.io/DropletQC/
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
biocViews:
Imports: 
    Rsamtools,
    stats,
    future,
    furrr,
    utils,
    GenomicRanges,
    ggplot2,
    dplyr,
    BiocGenerics,
    S4Vectors,
    GenomicAlignments,
    GenomicFeatures,
    rtracklayer,
    GenomeInfoDb,
    ks,
    ggpubr,
    mclust,
    stringr,
    patchwork
Suggests: 
    knitr,
    rmarkdown,
    markdown
VignetteBuilder: knitr
Depends: 
    R (>= 2.10)