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.
|Bioconductor views||Alignment ChIPSeq Coverage DataImport GeneExpression GeneSetEnrichment Genetics Infrastructure MethylSeq QualityControl RNASeq RiboSeq SNP Sequencing|
|Maintainer||Thomas Girke <firstname.lastname@example.org>|
|Package repository||View on Bioconductor|
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