Package: systemPipeR
Type: Package
Title: systemPipeR: NGS workflow and report generation environment
Version: 1.0.12
Date: 2015-02-23
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke@ucr.edu>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
        ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage,
        GeneSetEnrichment, Alignment, QualityControl
Description: R package for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. An important feature is support for running command-line software, such as NGS aligners, on both single machines or compute clusters. Instructions for using systemPipeR are given in the Overview Vignette (PDF). The remaining Vignettes, linked below, are workflow templates for common NGS use cases.
Depends: Rsamtools, Biostrings, ShortRead, methods
Imports: BiocGenerics, rjson, grid, ggplot2, limma, edgeR, DESeq2,
        GOstats, GO.db, annotate, pheatmap, BatchJobs
Suggests: ape, RUnit, BiocStyle, biomaRt, GenomicFeatures, BiocParallel
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
Packaged: 2015-03-25 04:50:01 UTC; biocbuild
Built: R 3.1.3; ; 2015-03-25 13:04:09 UTC; windows
