Package Recipe 'bioconductor-elmer'

recipe bioconductor-elmer

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/ELMER.html
License:: GPL-3
Recipe:: /bioconductor-elmer/meta.yaml

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¶

Versions:

2.33.1-0, 2.26.0-0, 2.24.1-0, 2.22.0-0, 2.18.0-0, 2.16.0-0, 2.14.0-1, 2.14.0-0, 2.12.0-0,

2.33.1-0, 2.26.0-0, 2.24.1-0, 2.22.0-0, 2.18.0-0, 2.16.0-0, 2.14.0-1, 2.14.0-0, 2.12.0-0, 2.9.5-1, 2.8.0-1, 2.6.1-0, 2.4.4-1, 2.4.4-0

Depends:

on bioconductor-biomart >=2.66.0,<2.67.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-elmer.data >=2.34.0,<2.35.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-gviz >=1.54.0,<1.55.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-tcgabiolinks >=2.38.0,<2.39.0
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-doparallel
on r-downloader
on r-dplyr
on r-ggplot2
on r-ggpubr
on r-ggrepel
on r-gridextra
on r-lattice
on r-magrittr
on r-matrix
on r-plotly
on r-plyr
on r-progress
on r-purrr
on r-readr
on r-reshape
on r-reshape2
on r-rmarkdown
on r-rvest
on r-scales
on r-stringr
on r-tibble
on r-tidyr
on r-xml2

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-elmer

to add into an existing workspace instead, run:

pixi add bioconductor-elmer

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-elmer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-elmer

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-elmer:<tag>

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