recipe bioconductor-elmer

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes






ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

package bioconductor-elmer

(downloads) docker_bioconductor-elmer



depends bioconductor-biomart:


depends bioconductor-complexheatmap:


depends bioconductor-delayedarray:




depends bioconductor-genomeinfodb:


depends bioconductor-genomicfeatures:


depends bioconductor-genomicranges:


depends bioconductor-gviz:


depends bioconductor-iranges:


depends bioconductor-multiassayexperiment:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends bioconductor-tcgabiolinks:


depends r-base:


depends r-circlize:

depends r-doparallel:

depends r-downloader:

depends r-dplyr:

depends r-ggplot2:

depends r-ggpubr:

depends r-ggrepel:

depends r-gridextra:

depends r-lattice:

depends r-magrittr:

depends r-matrix:

depends r-plotly:

depends r-plyr:

depends r-progress:

depends r-purrr:

depends r-readr:

depends r-reshape:

depends r-reshape2:

depends r-rmarkdown:

depends r-rvest:

depends r-scales:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-xml2:



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-elmer

and update with::

   mamba update bioconductor-elmer

To create a new environment, run:

mamba create --name myenvname bioconductor-elmer

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-elmer/tags`_ for valid values for ``<tag>``)

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