recipe bioconductor-methreg

Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MethReg.html

License:

GPL-3

Recipe:

/bioconductor-methreg/meta.yaml

Epigenome-wide association studies (EWAS) detects a large number of DNA methylation differences, often hundreds of differentially methylated regions and thousands of CpGs, that are significantly associated with a disease, many are located in non-coding regions. Therefore, there is a critical need to better understand the functional impact of these CpG methylations and to further prioritize the significant changes. MethReg is an R package for integrative modeling of DNA methylation, target gene expression and transcription factor binding sites data, to systematically identify and rank functional CpG methylations. MethReg evaluates, prioritizes and annotates CpG sites with high regulatory potential using matched methylation and gene expression data, along with external TF-target interaction databases based on manually curation, ChIP-seq experiments or gene regulatory network analysis.

package bioconductor-methreg

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.1-0,  1.0.0-2,  1.0.0-1

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-sesame:

>=1.20.0,<1.21.0

depends bioconductor-sesamedata:

>=1.20.0,<1.21.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-ggpubr:

depends r-mass:

depends r-matrix:

depends r-plyr:

depends r-progress:

depends r-pscl:

depends r-readr:

depends r-rlang:

depends r-sfsmisc:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

requirements:

Installation

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-methreg

and update with::

   mamba update bioconductor-methreg

To create a new environment, run:

mamba create --name myenvname bioconductor-methreg

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 quay.io/biocontainers/bioconductor-methreg:<tag>

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

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