Package Recipe 'bioconductor-rflomics'

recipe bioconductor-rflomics

Interactive web application for Omics-data analysis

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/RFLOMICS.html
License:: Artistic-2.0
Recipe:: /bioconductor-rflomics/meta.yaml

R-package with shiny interface, provides a framework for the analysis of transcriptomics, proteomics and/or metabolomics data. The interface offers a guided experience for the user, from the definition of the experimental design to the integration of several omics table together. A report can be generated with all settings and analysis results.

package bioconductor-rflomics¶

Versions:

1.2.0-0

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-clusterprofiler >=4.18.0,<4.19.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-coseq >=1.34.0,<1.35.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-enrichplot >=1.30.0,<1.31.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-mixomics >=6.34.0,<6.35.0
on bioconductor-mofa2 >=1.20.0,<1.21.0
on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-org.at.tair.db >=3.22.0,<3.23.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dplyr
on r-dt
on r-factominer
on r-ggplot2
on r-ggpubr
on r-ggrepel
on r-htmltools
on r-httr
on r-knitr
on r-magrittr
on r-plotly
on r-purrr
on r-rcolorbrewer
on r-reshape2
on r-reticulate
on r-rmarkdown
on r-shiny
on r-shinybs
on r-shinydashboard
on r-shinywidgets
on r-stringr
on r-tibble
on r-tidyr
on r-tidyselect
on r-upsetr
on r-vroom

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-rflomics

to add into an existing workspace instead, run:

pixi add bioconductor-rflomics

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-rflomics

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rflomics

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-rflomics:<tag>

(see bioconductor-rflomics/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-rflomics/README.html)