recipe bioconductor-methreg

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

Homepage:

https://bioconductor.org/packages/3.16/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:

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

Depends:

• bioconductor-annotationhub >=3.6.0,<3.7.0

• bioconductor-delayedarray >=0.24.0,<0.25.0

• bioconductor-experimenthub >=2.6.0,<2.7.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-sesame >=1.16.0,<1.17.0

• bioconductor-sesamedata >=1.16.0,<1.17.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-dplyr

• r-ggplot2

• r-ggpubr

• r-mass

• r-matrix

• r-plyr

• r-progress

• r-pscl

• r-readr

• r-rlang

• r-sfsmisc

• r-stringr

• r-tibble

• r-tidyr

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-methreg

and update with:

conda update bioconductor-methreg

or use the docker container:

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

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

Download stats

Link to this page

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