Package Recipe 'bioconductor-systempipetools'

recipe bioconductor-systempipetools

Tools for data visualization

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/systemPipeTools.html
License:: Artistic-2.0
Recipe:: /bioconductor-systempipetools/meta.yaml

systemPipeTools package extends the widely used systemPipeR (SPR) workflow environment with an enhanced toolkit for data visualization, including utilities to automate the data visualizaton for analysis of differentially expressed genes (DEGs). systemPipeTools provides data transformation and data exploration functions via scatterplots, hierarchical clustering heatMaps, principal component analysis, multidimensional scaling, generalized principal components, t-Distributed Stochastic Neighbor embedding (t-SNE), and MA and volcano plots. All these utilities can be integrated with the modular design of the systemPipeR environment that allows users to easily substitute any of these features and/or custom with alternatives.

package bioconductor-systempipetools¶

Versions:

1.18.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-ggtree >=4.0.0,<4.1.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-ape
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-dt
on r-ggally
on r-ggplot2
on r-ggrepel
on r-glmpca
on r-magrittr
on r-pheatmap
on r-plotly
on r-rtsne
on r-tibble

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-systempipetools

to add into an existing workspace instead, run:

pixi add bioconductor-systempipetools

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-systempipetools

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-systempipetools

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-systempipetools:<tag>

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