Package: systemPipeR
Type: Package
Title: systemPipeR: NGS workflow and report generation environment
Version: 1.4.8
Date: 2015-02-26
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke@ucr.edu>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
        RiboSeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage,
        GeneSetEnrichment, Alignment, QualityControl
Description: R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. Instructions for using systemPipeR are given in the Overview Vignette (HTML). The remaining Vignettes, linked below, are workflow templates for common NGS use cases.
Depends: Rsamtools, Biostrings, ShortRead, methods
Imports: BiocGenerics, GenomicRanges, GenomicFeatures,
        SummarizedExperiment, VariantAnnotation, rjson, grid, ggplot2,
        limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap,
        BatchJobs
Suggests: ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt,
        BiocParallel
VignetteBuilder: knitr
SystemRequirements: systemPipeR can be used to run external
        command-line software (e.g. short read aligners), but the
        corresponding tool needs to be installed on a system.
License: Artistic-2.0
URL: https://github.com/tgirke/systemPipeR
NeedsCompilation: no
Packaged: 2016-01-27 04:36:32 UTC; biocbuild
Built: R 3.2.2; ; 2016-05-02 16:05:50 UTC; unix
