DESCRIPTION

Package: scPipe
Title: Pipeline for single cell multi-omic data pre-processing
Date: 2022-10-12
Version: 1.99.2
Type: Package
Authors@R: c(person("Luyi", "Tian", role=c("aut"), email="tian.l@wehi.edu.au"), 
        person("Shian", "Su", role=c("aut", "cre"), email="su.s@wehi.edu.au"), 
        person("Shalin", "Naik", role=c("ctb"), email="naik.s@wehi.edu.au"), 
        person("Shani", "Amarasinghe", role=c("aut"), email="amarasinghe.s@wehi.edu.au"), 
        person("Oliver", "Voogd", role=c("aut"), email="voogd.o@wehi.edu.au"), 
        person("Phil", "Yang", role=c("aut"), email="yang.p@wehi.edu.au"), 
        person("Matthew", "Ritchie", role=c("ctb"), email="mritchie@wehi.edu.au"))
biocViews: ImmunoOncology, Software, Sequencing, RNASeq, GeneExpression, SingleCell, Visualization,
        SequenceMatching, Preprocessing, QualityControl, GenomeAnnotation, DataImport
Description: A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.
Depends:
    R (>= 4.2.0),
    SingleCellExperiment
LinkingTo:
    Rcpp,
    Rhtslib (>= 1.13.1),
    zlibbioc,
    testthat
Imports:
    AnnotationDbi,
    basilisk,
    BiocGenerics,
    biomaRt,
    Biostrings,
    data.table,
    dplyr,
    DropletUtils,
    flexmix,
    GenomicRanges,
    GenomicAlignments,
    GGally,
    ggplot2,
    glue (>= 1.3.0),
    grDevices,
    graphics,
    hash,
    IRanges,
    magrittr,
    MASS,
    Matrix (>= 1.5.0),
    mclust,
    methods,
    MultiAssayExperiment,
    org.Hs.eg.db,
    org.Mm.eg.db,
    purrr,
    Rcpp (>= 0.11.3),
    reshape,
    reticulate,
    Rhtslib,
    rlang,
    robustbase,
    Rsamtools,
    Rsubread,
    rtracklayer,
    SummarizedExperiment,
    S4Vectors,
    scales,
    stats,
    stringr,
    tibble,
    tidyr,
    tools,
    utils,
    vctrs (>= 0.5.2)
SystemRequirements: C++11, GNU make
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 7.2.3
NeedsCompilation: yes
URL: https://github.com/LuyiTian/scPipe
BugReports: https://github.com/LuyiTian/scPipe
Suggests: 
    BiocStyle,
    DT,
    GenomicFeatures,
    grid,
    igraph,
    kableExtra,
    knitr,
    locStra,
    plotly,
    rmarkdown,
    RColorBrewer,
    readr,
    reshape2,
    RANN,
    shiny,
    scater (>= 1.11.0),
    testthat,
    xml2,
    umap
VignetteBuilder: knitr