Package Recipe 'bioconductor-ramwas'

recipe bioconductor-ramwas

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Homepage:: https://bioconductor.org/packages/3.20/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:

1.34.0-0, 1.30.0-0, 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,

1.34.0-0, 1.30.0-0, 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:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-biomart >=2.66.0,<2.67.0
on bioconductor-biomart >=2.66.0,<2.67.0a0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-biostrings >=2.78.0,<2.79.0a0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0a0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-digest
on r-filematrix
on r-glmnet
on r-kernsmooth

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-ramwas

to add into an existing workspace instead, run:

pixi add bioconductor-ramwas

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-ramwas

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-ramwas

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-ramwas:<tag>

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