Package: scPipe
Title: pipeline for single cell RNA-seq data analysis
Date: 2018-04-26
Version: 1.2.1
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: 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 (>= 1.12.1), zlibbioc
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
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 6.0.1
NeedsCompilation: yes
URL: https://github.com/LuyiTian/scPipe
BugReports: https://github.com/LuyiTian/scPipe
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Packaged: 2018-06-02 04:13:14 UTC; biocbuild
Built: R 3.5.0; i386-w64-mingw32; 2018-06-02 12:47:13 UTC; windows
Archs: i386, x64
