recipe bioconductor-ioniser

Quality Assessment Tools for Oxford Nanopore MinION data

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/IONiseR.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-ioniser/meta.yaml

Links:

biotools: ioniser, doi: 10.1038/nmeth.3252

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

package bioconductor-ioniser

versions:

2.24.0-0,  2.22.0-0,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.12.0-0,  2.10.0-0,  2.8.0-1, 

2.24.0-0,  2.22.0-0,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.12.0-0,  2.10.0-0,  2.8.0-1,  2.6.0-0,  2.4.0-0,  2.2.0-0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-rhdf5:

>=2.44.0,<2.45.0

depends bioconductor-shortread:

>=1.58.0,<1.59.0

depends bioconductor-xvector:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bit64:

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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-ioniser

and update with::

   mamba update bioconductor-ioniser

To create a new environment, run:

mamba create --name myenvname bioconductor-ioniser

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-ioniser:<tag>

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

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-ioniser/README.html)