systemPipeR

Package: systemPipeR
Type: Package
Title: systemPipeR: NGS workflow and report generation environment
Version: 1.6.2
Date: 2016-02-26
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, ggplot2, grid,
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: 2016-05-16 04:51:50 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'systemPipeR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'systemPipeR'
    finding HTML links ... done
    GOHyperGAll                             html  
    INTERSECTset-class                      html  
    SYSargs-class                           html  
    VENNset-class                           html  
    alignStats                              html  
    catDB-class                             html  
    catmap                                  html  
    clusterRun                              html  
    countRangeset                           html  
    featureCoverage                         html  
    featuretypeCounts                       html  
    filterDEGs                              html  
    filterVars                              html  
    genFeatures                             html  
    getQsubargs                             html  
    mergeBamByFactor                        html  
    moduleload                              html  
    olBarplot                               html  
    overLapper                              html  
    plotfeatureCoverage                     html  
    plotfeaturetypeCounts                   html  
    predORF                                 html  
    preprocessReads                         html  
    qsubRun                                 html  
    readComp                                html  
    returnRPKM                              html  
    runCommandline                          html  
    runDiff                                 html  
    run_DESeq2                              html  
    run_edgeR                               html  
    scaleRanges                             html  
    seeFastq                                html  
    symLink2bam                             html  
    sysargs                                 html  
    systemArgs                              html  
    variantReport                           html  
    vennPlot                                html  
    writeTargetsRef                         html  
    writeTargetsout                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (systemPipeR)
Making 'packages.html' ... done