Package Recipe 'bioconductor-gdcrnatools'

recipe bioconductor-gdcrnatools

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/GDCRNATools.html
License:: Artistic-2.0
Recipe:: /bioconductor-gdcrnatools/meta.yaml

This is an easy-to-use package for downloading, organizing, and integrative analyzing RNA expression data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer. Three databases of lncRNA-miRNA interactions including spongeScan, starBase, and miRcode, as well as three databases of mRNA-miRNA interactions including miRTarBase, starBase, and miRcode are incorporated into the package for ceRNAs network construction. limma, edgeR, and DESeq2 can be used to identify differentially expressed genes/miRNAs. Functional enrichment analyses including GO, KEGG, and DO can be performed based on the clusterProfiler and DO packages. Both univariate CoxPH and KM survival analyses of multiple genes can be implemented in the package. Besides some routine visualization functions such as volcano plot, bar plot, and KM plot, a few simply shiny apps are developed to facilitate visualization of results on a local webpage.

package bioconductor-gdcrnatools¶

Versions:

1.30.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.1-0, 1.10.0-0,

1.30.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.1-0, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.2.0-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biomart >=2.66.0,<2.67.0
on bioconductor-clusterprofiler >=4.18.0,<4.19.0
on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-dose >=4.4.0,<4.5.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-genomicdatacommons >=1.34.0,<1.35.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0
on bioconductor-pathview >=1.50.0,<1.51.0
on r-base >=4.5,<4.6.0a0
on r-dt
on r-ggplot2
on r-gplots
on r-jsonlite
on r-rjson
on r-shiny
on r-survival
on r-survminer
on r-xml

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-gdcrnatools

to add into an existing workspace instead, run:

pixi add bioconductor-gdcrnatools

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-gdcrnatools

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-gdcrnatools

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-gdcrnatools:<tag>

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