Package Recipe 'bioconductor-cemitool'

recipe bioconductor-cemitool

Co-expression Modules identification Tool

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/CEMiTool.html
License:: GPL-3
Recipe:: /bioconductor-cemitool/meta.yaml

The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.

package bioconductor-cemitool¶

Versions:

1.34.0-0, 1.30.0-0, 1.26.0-0, 1.24.0-0, 1.22.0-0, 1.18.1-0, 1.16.0-0, 1.14.1-0, 1.14.0-0,

1.34.0-0, 1.30.0-0, 1.26.0-0, 1.24.0-0, 1.22.0-0, 1.18.1-0, 1.16.0-0, 1.14.1-0, 1.14.0-0, 1.12.0-0, 1.10.0-0, 1.8.3-0, 1.6.10-0

Depends:

on bioconductor-clusterprofiler >=4.18.0,<4.19.0
on bioconductor-fgsea >=1.36.0,<1.37.0
on r-base >=4.5,<4.6.0a0
on r-data.table >=1.9.4
on r-dplyr
on r-dt
on r-fastcluster
on r-ggdendro
on r-ggplot2
on r-ggpmisc
on r-ggrepel
on r-ggthemes
on r-gridextra
on r-gtable
on r-htmltools
on r-igraph
on r-intergraph
on r-knitr
on r-matrixstats
on r-network
on r-pracma
on r-rmarkdown
on r-scales
on r-sna
on r-stringr
on r-wgcna

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-cemitool

to add into an existing workspace instead, run:

pixi add bioconductor-cemitool

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-cemitool

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cemitool

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-cemitool:<tag>

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