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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR@112915 bc3139a8-67e5-0310-9ffc-ced21a209358
tgirke · Jan 26, 2016 · 754e215 · 754e215
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -8,7 +8,7 @@ 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
+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.

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,5 @@
 ## IMPORTS
-import(rjson, GenomicRanges, GenomicFeatures, SummarizedExperiment, Rsamtools, Biostrings, ShortRead, grid, ggplot2, limma, edgeR, GOstats, GO.db, annotate, pheatmap, BatchJobs, methods)
+import(rjson, GenomicRanges, GenomicFeatures, SummarizedExperiment, Rsamtools, Biostrings, ShortRead, ggplot2, grid, limma, edgeR, GOstats, GO.db, annotate, pheatmap, BatchJobs, methods)
 ## S4 Classes
 exportClasses(
     "SYSargs", "catDB", "VENNset", "INTERSECTset"