recipe bioconductor-timirgen

Time sensitive microRNA-mRNA integration, analysis and network generation tool

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/TimiRGeN.html

License:

GPL-3

Recipe:

/bioconductor-timirgen/meta.yaml

TimiRGeN (Time Incorporated miR-mRNA Generation of Networks) is a novel R package which functionally analyses and integrates time course miRNA-mRNA differential expression data. This tool can generate small networks within R or export results into cytoscape or pathvisio for more detailed network construction and hypothesis generation. This tool is created for researchers that wish to dive deep into time series multi-omic datasets. TimiRGeN goes further than many other tools in terms of data reduction. Here, potentially hundreds-of-thousands of potential miRNA-mRNA interactions can be whittled down into a handful of high confidence miRNA-mRNA interactions affecting a signalling pathway, across a time course.

package bioconductor-timirgen

versions:

1.11.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.3-0,  1.0.0-0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-clusterprofiler:

>=4.10.0,<4.11.0

depends bioconductor-mfuzz:

>=2.62.0,<2.63.0

depends bioconductor-multiassayexperiment:

>=1.28.0,<1.29.0

depends bioconductor-rcy3:

>=2.22.0,<2.23.0

depends bioconductor-rwikipathways:

>=1.22.0,<1.23.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

>=0.8.4

depends r-freqprof:

depends r-ggdendro:

depends r-gghighlight:

depends r-ggplot2:

depends r-gplots:

depends r-gtools:

>=3.8.1

depends r-igraph:

>=1.2.4.2

depends r-readxl:

depends r-reshape2:

depends r-scales:

depends r-stringr:

>=1.4.0

depends r-tidyr:

>=1.0.2

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-timirgen

and update with::

   mamba update bioconductor-timirgen

To create a new environment, run:

mamba create --name myenvname bioconductor-timirgen

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-timirgen:<tag>

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

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Link to this page

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