Package Recipe 'bioconductor-methodical'

recipe bioconductor-methodical

Discovering genomic regions where methylation is strongly associated with transcriptional activity

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/methodical.html
License:: GPL (>= 3)
Recipe:: /bioconductor-methodical/meta.yaml

DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.

package bioconductor-methodical¶

Versions:

1.6.0-0

Depends:

on bioconductor-annotationhub >=4.0.0,<4.1.0
on bioconductor-annotatr >=1.36.0,<1.37.0
on bioconductor-bioccheck >=1.46.0,<1.47.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biocstyle >=2.38.0,<2.39.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0
on bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-experimenthub >=3.0.0,<3.1.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-hdf5array >=1.38.0,<1.39.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-matrixgenerics >=1.22.0,<1.23.0
on bioconductor-rhdf5 >=2.54.0,<2.55.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-tumourmethdata >=1.8.0,<1.9.0
on r-base >=4.5,<4.6.0a0
on r-biocmanager
on r-cowplot
on r-data.table
on r-devtools
on r-dplyr
on r-foreach
on r-ggplot2
on r-knitr
on r-r.utils
on r-rcmdcheck
on r-rcpproll
on r-remotes
on r-scales
on r-tibble
on r-tidyr
on r-usethis

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-methodical

to add into an existing workspace instead, run:

pixi add bioconductor-methodical

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-methodical

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-methodical

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-methodical:<tag>

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