recipe bioconductor-systempipetools

Tools for data visualization

Homepage:

https://bioconductor.org/packages/3.18/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:

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

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-ggtree:

>=3.10.0,<3.11.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-dt:

depends r-ggally:

depends r-ggplot2:

depends r-ggrepel:

depends r-glmpca:

depends r-magrittr:

depends r-pheatmap:

depends r-plotly:

depends r-rtsne:

depends r-tibble:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-systempipetools

and update with::

   mamba update bioconductor-systempipetools

To create a new environment, run:

mamba create --name myenvname bioconductor-systempipetools

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-systempipetools/tags`_ for valid values for ``<tag>``)

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