recipe bioconductor-hireewas

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

Homepage:

https://bioconductor.org/packages/3.20/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:
1.28.0-0,  1.24.0-0,  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, 

1.28.0-0,  1.24.0-0,  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:

  • 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-gplots

  • on r-quadprog

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-hireewas

to add into an existing workspace instead, run:

pixi add bioconductor-hireewas

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-hireewas

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-hireewas

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-hireewas:<tag>

(see bioconductor-hireewas/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.

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