Package Recipe 'bioconductor-methylscaper'

recipe bioconductor-methylscaper

Visualization of Methylation Data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/methylscaper.html
License:: GPL-2
Recipe:: /bioconductor-methylscaper/meta.yaml

methylscaper is an R package for processing and visualizing data jointly profiling methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package supports both single-cell and single-molecule data, and a common interface for jointly visualizing both data types through the generation of ordered representational methylation-state matrices. The Shiny app allows for an interactive seriation process of refinement and re-weighting that optimally orders the cells or DNA molecules to discover methylation patterns and nucleosome positioning.

package bioconductor-methylscaper¶

Versions:

1.18.0-0, 1.14.0-0, 1.10.0-0, 1.8.4-0, 1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-pwalign >=1.6.0,<1.7.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-rfast
on r-seqinr
on r-seriation
on r-shiny
on r-shinyfiles
on r-shinyjs

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-methylscaper

to add into an existing workspace instead, run:

pixi add bioconductor-methylscaper

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-methylscaper

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-methylscaper

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-methylscaper:<tag>

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