Package Recipe 'bioconductor-smartphos'

recipe bioconductor-smartphos

A phosphoproteomics data analysis package with an interactive ShinyApp

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/SmartPhos.html
License:: GPL-3
Recipe:: /bioconductor-smartphos/meta.yaml

To facilitate and streamline phosphoproteomics data analysis, we developed SmartPhos, an R package for the pre-processing, quality control, and exploratory analysis of phosphoproteomics data generated by MaxQuant and Spectronaut. The package can be used either through the R command line or through an interactive ShinyApp called SmartPhos Explorer. The package contains methods such as normalization and normalization correction, transformation, imputation, batch effect correction, PCA, heatmap, differential expression, time-series clustering, gene set enrichment analysis, and kinase activity inference.

package bioconductor-smartphos¶

Versions:

1.0.0-0

Depends:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-decoupler >=2.16.0,<2.17.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-mscoreutils >=1.22.0,<1.23.0
on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-piano >=2.26.0,<2.27.0
on bioconductor-proda >=1.24.0,<1.25.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-vsn >=3.78.0,<3.79.0
on r-base >=4.5,<4.6.0a0
on r-cowplot
on r-data.table
on r-doparallel
on r-dorng
on r-dplyr
on r-dt
on r-e1071
on r-factoextra
on r-ggbeeswarm
on r-ggplot2
on r-imputelcmd
on r-magrittr
on r-matrixstats
on r-missforest
on r-pheatmap
on r-plotly
on r-rlang
on r-shiny
on r-shinybs
on r-shinyjs
on r-shinythemes
on r-shinywidgets
on r-stringr
on r-tibble
on r-tidyr
on r-xml

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-smartphos

to add into an existing workspace instead, run:

pixi add bioconductor-smartphos

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-smartphos

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-smartphos

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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-smartphos/README.html)