Package Recipe 'bioconductor-cohcap'

recipe bioconductor-cohcap

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/COHCAP.html
License:: GPL-3.0-only
Recipe:: /bioconductor-cohcap/meta.yaml
Links:: biotools: cohcap

COHCAP (pronounced "co-cap") provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options. Discussion Group: https://sourceforge.net/p/cohcap/discussion/bioconductor/

package bioconductor-cohcap¶

Versions:

1.48.0-1, 1.48.0-0, 1.46.0-0, 1.44.0-1, 1.44.0-0, 1.40.0-3, 1.40.0-2, 1.40.0-1, 1.40.0-0,

1.48.0-1, 1.48.0-0, 1.46.0-0, 1.44.0-1, 1.44.0-0, 1.40.0-3, 1.40.0-2, 1.40.0-1, 1.40.0-0, 1.38.0-0, 1.36.0-1, 1.36.0-0, 1.34.1-0, 1.32.0-1, 1.30.0-1, 1.30.0-0, 1.28.1-0, 1.26.0-0, 1.24.0-0

Depends:

on bioconductor-cohcapanno >=1.38.0,<1.39.0
on bioconductor-cohcapanno >=1.38.0,<1.39.0a0
on libblas >=3.9.0,<4.0a0
on libgcc-ng >=12
on liblapack >=3.9.0,<4.0a0
on libstdcxx-ng >=12
on perl >=5.32.1,<5.33.0a0 *_perl5
on perl >=5.6.0
on r-base >=4.3,<4.4.0a0
on r-bh
on r-gplots
on r-rcolorbrewer
on r-rcpp
on r-rcpparmadillo
on r-writexls

Additional platforms:

linux-aarch64

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-cohcap

to add into an existing workspace instead, run:

pixi add bioconductor-cohcap

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-cohcap

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cohcap

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-cohcap:<tag>

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