Package Recipe 'bioconductor-transcriptogramer'

recipe bioconductor-transcriptogramer

Transcriptional analysis based on transcriptograms

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/transcriptogramer.html
License:: GPL (>= 2)
Recipe:: /bioconductor-transcriptogramer/meta.yaml

R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered.

package bioconductor-transcriptogramer¶

Versions:

1.32.0-0, 1.28.0-0, 1.24.0-0, 1.22.0-0, 1.20.0-0, 1.16.0-0, 1.14.0-0, 1.12.0-1, 1.12.0-0,

1.32.0-0, 1.28.0-0, 1.24.0-0, 1.22.0-0, 1.20.0-0, 1.16.0-0, 1.14.0-0, 1.12.0-1, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.4.1-0

Depends:

on bioconductor-biomart >=2.66.0,<2.67.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-reder >=3.6.0,<3.7.0
on bioconductor-topgo >=2.62.0,<2.63.0
on openjdk
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dosnow
on r-foreach
on r-ggplot2
on r-igraph
on r-progress
on r-snow
on r-tidyr

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-transcriptogramer

to add into an existing workspace instead, run:

pixi add bioconductor-transcriptogramer

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-transcriptogramer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-transcriptogramer

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-transcriptogramer:<tag>

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