Package Recipe 'bioconductor-ioniser'

recipe bioconductor-ioniser

Quality Assessment Tools for Oxford Nanopore MinION data

Homepage:: https://bioconductor.org/packages/3.20/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:

2.34.0-0, 2.30.0-0, 2.26.0-0, 2.24.0-0, 2.22.0-0, 2.18.0-0, 2.16.0-0, 2.14.0-1, 2.14.0-0,

2.34.0-0, 2.30.0-0, 2.26.0-0, 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:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-rhdf5 >=2.54.0,<2.55.0
on bioconductor-shortread >=1.68.0,<1.69.0
on bioconductor-xvector >=0.50.0,<0.51.0
on r-base >=4.5,<4.6.0a0
on r-bit64
on r-dplyr
on r-ggplot2
on r-magrittr
on r-stringr
on r-tibble
on r-tidyr

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-ioniser

to add into an existing workspace instead, run:

pixi add bioconductor-ioniser

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-ioniser

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-ioniser

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-ioniser:<tag>

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