recipe bioconductor-timirgen

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

Homepage

https://bioconductor.org/packages/3.14/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

1.4.0-0,  1.2.0-0,  1.0.3-0,  1.0.0-0

Depends

• bioconductor-biomart >=2.50.0,<2.51.0

• bioconductor-clusterprofiler >=4.2.0,<4.3.0

• bioconductor-mfuzz >=2.54.0,<2.55.0

• bioconductor-multiassayexperiment >=1.20.0,<1.21.0

• bioconductor-rcy3 >=2.14.0,<2.15.0

• bioconductor-rwikipathways >=1.14.0,<1.15.0

• r-base >=4.1,<4.2.0a0

• r-dplyr >=0.8.4

• r-freqprof

• r-ggdendro

• r-gghighlight

• r-ggplot2

• r-gplots

• r-gtools >=3.8.1

• r-igraph >=1.2.4.2

• r-readxl

• r-reshape2

• r-scales

• r-stringr >=1.4.0

• r-tidyr >=1.0.2

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-timirgen

and update with:

conda update bioconductor-timirgen

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-timirgen:<tag>

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

Download stats

Link to this page

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