bioconductor-systempiper

Summary

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.

Versions

  • 1.4.7

License

Artistic-2.0

Meta

package:
  name: bioconductor-systempiper
  version: 1.4.7

source:
  fn: systemPipeR_1.4.7.tar.gz
  url: http://bioconductor.org/packages/release/bioc/src/contrib/systemPipeR_1.4.7.tar.gz
  md5: 501b1bd634eb4844864f881056b9b471

build:
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/

requirements:
  build:
    - bioconductor-annotate
    - bioconductor-biocgenerics
    - bioconductor-biostrings
    - bioconductor-deseq2
    - bioconductor-edger
    - bioconductor-genomicfeatures
    - bioconductor-genomicranges
    - bioconductor-go.db
    - bioconductor-gostats
    - bioconductor-limma
    - bioconductor-rsamtools
    - bioconductor-shortread
    - bioconductor-summarizedexperiment
    - bioconductor-variantannotation
    - r
    - r-batchjobs
    - r-ggplot2
    - r-pheatmap
    - r-rjson
  run:
    - bioconductor-annotate
    - bioconductor-biocgenerics
    - bioconductor-biostrings
    - bioconductor-deseq2
    - bioconductor-edger
    - bioconductor-genomicfeatures
    - bioconductor-genomicranges
    - bioconductor-go.db
    - bioconductor-gostats
    - bioconductor-limma
    - bioconductor-rsamtools
    - bioconductor-shortread
    - bioconductor-summarizedexperiment
    - bioconductor-variantannotation
    - r
    - r-batchjobs
    - r-ggplot2
    - r-pheatmap
    - r-rjson

test:
  commands:
    - '$R -e "library(''systemPipeR'')"'

about:
  home: http://bioconductor.org/packages/release/bioc/html/systemPipeR.html
  license: Artistic-2.0
  summary: '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.'