recipe bioconductor-hireewas

Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-hireewas/meta.yaml

In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. The current approaches to the association detection only claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not, but they cannot determine the cell type in which the risk-CpG site is affected by the phenotype. We propose a solid statistical method, HIgh REsolution (HIRE), which not only substantially improves the power of association detection at the aggregated level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types. The "HIREewas" R package is to implement HIRE model in R.

package bioconductor-hireewas

(downloads) docker_bioconductor-hireewas

versions:
1.20.0-0,  1.18.0-0,  1.16.0-2,  1.16.0-1,  1.16.0-0,  1.12.0-2,  1.12.0-1,  1.12.0-0,  1.10.0-0, 

1.20.0-0,  1.18.0-0,  1.16.0-2,  1.16.0-1,  1.16.0-0,  1.12.0-2,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.2-0

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-gplots:

depends r-quadprog:

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-hireewas

and update with::

   mamba update bioconductor-hireewas

To create a new environment, run:

mamba create --name myenvname bioconductor-hireewas

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-hireewas:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda 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-hireewas/README.html)