recipe bioconductor-pcaexplorer

Interactive Visualization of RNA-seq Data Using a Principal Components Approach

Homepage

https://bioconductor.org/packages/3.11/bioc/html/pcaExplorer.html

License

MIT + file LICENSE

Recipe

/bioconductor-pcaexplorer/meta.yaml

Links

biotools: pcaexplorer, doi: 10.18547/gcb.2017.vol3.iss1.e39

This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.

package bioconductor-pcaexplorer

Versions

2.14.0-0,  2.12.0-0,  2.10.0-1,  2.8.0-0,  2.6.0-0,  2.4.0-0,  2.2.1-0,  2.0.0-0

Depends

• bioconductor-annotationdbi >=1.50.0,<1.51.0

• bioconductor-biomart >=2.44.0,<2.45.0

• bioconductor-deseq2 >=1.28.0,<1.29.0

• bioconductor-genefilter >=1.70.0,<1.71.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-go.db >=3.11.0,<3.12.0

• bioconductor-gostats >=2.54.0,<2.55.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-limma >=3.44.0,<3.45.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• bioconductor-topgo >=2.40.0,<2.41.0

• r-base >=4.0,<4.1.0a0

• r-base64enc

• r-d3heatmap

• r-dt

• r-ggplot2 >=2.0.0

• r-ggrepel

• r-knitr

• r-nmf

• r-pheatmap

• r-plyr

• r-rmarkdown

• r-scales

• r-shiny >=0.12.0

• r-shinyace

• r-shinybs

• r-shinydashboard

• r-threejs

• r-tidyr

Required By

• bioconductor-ideal

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-pcaexplorer

and update with:

conda update bioconductor-pcaexplorer

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-pcaexplorer:<tag>

(see bioconductor-pcaexplorer/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-pcaexplorer/README.html)