DESCRIPTION

Package: scPipe
Title: pipeline for single cell RNA-seq data analysis
Date: 2019-10-12
Version: 1.9.4
Type: Package
Maintainer: Luyi Tian <tian.l@wehi.edu.au>
Author: Luyi Tian
Authors@R: c(person("Luyi", "Tian", role=c("aut", "cre"),
        email="tian.l@wehi.edu.au"), person("Shian", "Su",
        role=c("aut"), email="su.s@wehi.edu.au"), person("Shalin",
        "Naik", role=c("ctb"),
        email="naik.s@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
Description: A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene 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 (>= 3.4),
    ggplot2,
    methods,
    SingleCellExperiment
LinkingTo:
    Rcpp,
    Rhtslib (>= 1.13.1),
    zlibbioc,
    testthat
Imports:
    Rhtslib,
    biomaRt,
    GGally,
    MASS,
    mclust,
    Rcpp (>= 0.11.3),
    reshape,
    BiocGenerics,
    robustbase,
    scales,
    utils,
    stats,
    S4Vectors,
    SummarizedExperiment,
    AnnotationDbi,
    org.Hs.eg.db,
    org.Mm.eg.db,
    stringr,
    rtracklayer,
    hash,
    dplyr,
    GenomicRanges,
    magrittr,
    glue (>= 1.3.0),
    rlang,
    scater (>= 1.11.0)
SystemRequirements: C++11, GNU make
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 6.1.1
NeedsCompilation: yes
URL: https://github.com/LuyiTian/scPipe
BugReports: https://github.com/LuyiTian/scPipe
Suggests: Rsubread, knitr, rmarkdown, testthat
VignetteBuilder: knitr