- recipe bioconductor-systempiper
systemPipeR: NGS workflow and report generation environment
- Homepage:
https://bioconductor.org/packages/3.14/bioc/html/systemPipeR.html
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: systempiper
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.
- package bioconductor-systempiper¶
-
- Versions:
2.0.0-0
,1.26.2-0
,1.24.3-0
,1.24.2-0
,1.22.0-0
,1.20.0-0
,1.18.2-0
,1.16.0-0
,1.14.0-0
,2.0.0-0
,1.26.2-0
,1.24.3-0
,1.24.2-0
,1.22.0-0
,1.20.0-0
,1.18.2-0
,1.16.0-0
,1.14.0-0
,1.12.0-0
,1.10.2-0
,1.9.0-0
,1.4.8-0
,1.4.7-0
- Depends:
bioconductor-biocgenerics
>=0.40.0,<0.41.0
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-shortread
>=1.52.0,<1.53.0
bioconductor-summarizedexperiment
>=1.24.0,<1.25.0
r-base
>=4.1,<4.2.0a0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-systempiper
and update with:
conda update bioconductor-systempiper
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-systempiper:<tag>
(see bioconductor-systempiper/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-systempiper/README.html)