recipe bioconductor-transcriptogramer

Transcriptional analysis based on transcriptograms

Homepage:

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

(downloads) docker_bioconductor-transcriptogramer

versions:
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, 

1.24.0-0,  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 bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-reder:

>=2.6.0,<2.7.0

depends bioconductor-topgo:

>=2.54.0,<2.55.0

depends openjdk:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dosnow:

depends r-foreach:

depends r-ggplot2:

depends r-igraph:

depends r-progress:

depends r-snow:

depends r-tidyr:

requirements:

additional platforms:

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-transcriptogramer

and update with::

   mamba update bioconductor-transcriptogramer

To create a new environment, run:

mamba create --name myenvname bioconductor-transcriptogramer

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-transcriptogramer:<tag>

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

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Link to this page

Render an install-with-bioconda 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)