recipe bioconductor-methylscaper

Visualization of Methylation Data

Homepage:

https://bioconductor.org/packages/3.18/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:

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

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-rfast:

depends r-seqinr:

depends r-seriation:

depends r-shiny:

depends r-shinyfiles:

depends r-shinyjs:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-methylscaper

and update with::

   mamba update bioconductor-methylscaper

To create a new environment, run:

mamba create --name myenvname bioconductor-methylscaper

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-methylscaper:<tag>

(see `bioconductor-methylscaper/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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