Package Recipe 'bioconductor-nanomethviz'

recipe bioconductor-nanomethviz

Visualise methylation data from Oxford Nanopore sequencing

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/NanoMethViz.html
License:: Apache License (>= 2.0)
Recipe:: /bioconductor-nanomethviz/meta.yaml

NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.

package bioconductor-nanomethviz¶

Versions:

3.6.0-0, 3.2.0-0, 2.8.1-0, 2.6.0-0, 2.4.0-1, 2.4.0-0, 2.0.0-2, 2.0.0-1, 2.0.0-0,

3.6.0-0, 3.2.0-0, 2.8.1-0, 2.6.0-0, 2.4.0-1, 2.4.0-0, 2.0.0-2, 2.0.0-1, 2.0.0-0, 1.2.0-0, 1.0.0-2, 1.0.0-1

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-annotationdbi >=1.72.0,<1.73.0a0
on bioconductor-biocsingular >=1.26.0,<1.27.0
on bioconductor-biocsingular >=1.26.1,<1.27.0a0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-biostrings >=2.78.0,<2.79.0a0
on bioconductor-bsseq >=1.46.0,<1.47.0
on bioconductor-bsseq >=1.46.0,<1.47.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-limma >=3.66.0,<3.67.0a0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on libblas >=3.9.0,<4.0a0
on libcxx >=19
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-assertthat
on r-base >=4.5,<4.6.0a0
on r-cli
on r-cpp11 >=0.2.5
on r-dbscan
on r-dplyr
on r-e1071
on r-forcats
on r-fs
on r-ggplot2 >=3.4.0
on r-ggrastr
on r-glue
on r-patchwork
on r-purrr
on r-r.utils
on r-rcpp
on r-readr
on r-rlang
on r-scales >=1.2.0
on r-stringr
on r-tibble
on r-tidyr
on r-withr

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-nanomethviz

to add into an existing workspace instead, run:

pixi add bioconductor-nanomethviz

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-nanomethviz

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-nanomethviz

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-nanomethviz:<tag>

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