Package: scPipe
Title: pipeline for single cell RNA-seq data analysis
Date: 2019-10-12
Version: 1.14.0
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
git_url: https://git.bioconductor.org/packages/scPipe
git_branch: RELEASE_3_13
git_last_commit: 998ffca
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
Packaged: 2021-05-19 22:49:26 UTC; biocbuild
Built: R 4.1.0; x86_64-apple-darwin13.4.0; 2021-06-01 09:06:18 UTC; unix
