Package Recipe 'bioconductor-timirgen'

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:

on bioconductor-biomart >=2.58.0,<2.59.0
on bioconductor-clusterprofiler >=4.10.0,<4.11.0
on bioconductor-mfuzz >=2.62.0,<2.63.0
on bioconductor-multiassayexperiment >=1.28.0,<1.29.0
on bioconductor-rcy3 >=2.22.0,<2.23.0
on bioconductor-rwikipathways >=1.22.0,<1.23.0
on r-base >=4.3,<4.4.0a0
on r-dplyr >=0.8.4
on r-freqprof
on r-ggdendro
on r-gghighlight
on r-ggplot2
on r-gplots
on r-gtools >=3.8.1
on r-igraph >=1.2.4.2
on r-readxl
on r-reshape2
on r-scales
on r-stringr >=1.4.0
on r-tidyr >=1.0.2

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-timirgen

to add into an existing workspace instead, run:

pixi add bioconductor-timirgen

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-timirgen

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-timirgen

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-timirgen:<tag>

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