recipe bioconductor-ramwas

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Homepage:

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

License:

LGPL-3

Recipe:

/bioconductor-ramwas/meta.yaml

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>.

package bioconductor-ramwas

versions:

1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.18.0-2,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-1, 

1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.18.0-2,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.6.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0a0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0a0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-digest:

depends r-filematrix:

depends r-glmnet:

depends r-kernsmooth:

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-ramwas

and update with::

   mamba update bioconductor-ramwas

To create a new environment, run:

mamba create --name myenvname bioconductor-ramwas

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-ramwas:<tag>

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

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