Package Recipe 'bioconductor-methylumi'

recipe bioconductor-methylumi

Handle Illumina methylation data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/methylumi.html
License:: GPL-2
Recipe:: /bioconductor-methylumi/meta.yaml
Links:: biotools: methylumi, doi: 10.1186/1471-2164-14-293

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

package bioconductor-methylumi¶

Versions:

2.56.0-0, 2.52.0-0, 2.48.0-0, 2.46.0-0, 2.44.0-0, 2.40.1-0, 2.38.0-0, 2.36.0-1, 2.36.0-0,

2.56.0-0, 2.52.0-0, 2.48.0-0, 2.46.0-0, 2.44.0-0, 2.40.1-0, 2.38.0-0, 2.36.0-1, 2.36.0-0, 2.34.0-0, 2.32.0-0, 2.30.0-1, 2.28.0-0, 2.26.0-0, 2.24.1-0, 2.22.0-1, 2.22.0-0

Depends:

on bioconductor-annotate >=1.88.0,<1.89.0
on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0
on bioconductor-genefilter >=1.92.0,<1.93.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-illuminaio >=0.52.0,<0.53.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-minfi >=1.56.0,<1.57.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-ggplot2
on r-lattice
on r-matrixstats
on r-reshape2
on r-scales

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-methylumi

to add into an existing workspace instead, run:

pixi add bioconductor-methylumi

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-methylumi

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-methylumi

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-methylumi:<tag>

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