recipe bioconductor-gdcrnatools

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






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

(downloads) docker_bioconductor-gdcrnatools



depends bioconductor-biocparallel:


depends bioconductor-biomart:


depends bioconductor-clusterprofiler:


depends bioconductor-deseq2:


depends bioconductor-dose:


depends bioconductor-edger:


depends bioconductor-genomicdatacommons:


depends bioconductor-limma:




depends bioconductor-pathview:


depends r-base:


depends r-dt:

depends r-ggplot2:

depends r-gplots:

depends r-jsonlite:

depends r-rjson:

depends r-shiny:

depends r-survival:

depends r-survminer:

depends r-xml:



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-gdcrnatools

and update with::

   mamba update bioconductor-gdcrnatools

To create a new environment, run:

mamba create --name myenvname bioconductor-gdcrnatools

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<tag>

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

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