recipe bioconductor-ramwas

A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) <doi:10.1093/bioinformatics/bty069>.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/ramwas.html

License

LGPL-3

Recipe

/bioconductor-ramwas/meta.yaml

package bioconductor-ramwas

(downloads) docker_bioconductor-ramwas

Versions

1.6.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-ramwas

and update with:

conda update bioconductor-ramwas

or use the docker container:

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

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