Package Recipe 'bioconductor-r453plus1toolbox'

recipe bioconductor-r453plus1toolbox

A package for importing and analyzing data from Roche's Genome Sequencer System

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/R453Plus1Toolbox.html
License:: LGPL-3
Recipe:: /bioconductor-r453plus1toolbox/meta.yaml

The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.

package bioconductor-r453plus1toolbox¶

Versions:

1.56.0-0, 1.52.0-0, 1.50.0-0, 1.48.0-1, 1.48.0-0, 1.44.0-2, 1.44.0-1, 1.44.0-0, 1.42.0-0,

1.56.0-0, 1.52.0-0, 1.50.0-0, 1.48.0-1, 1.48.0-0, 1.44.0-2, 1.44.0-1, 1.44.0-0, 1.42.0-0, 1.40.0-1, 1.40.0-0, 1.38.0-0, 1.36.0-0, 1.34.0-1, 1.32.0-0

Depends:

on bioconductor-biobase >=2.66.0,<2.67.0
on bioconductor-biobase >=2.66.0,<2.67.0a0
on bioconductor-biocgenerics >=0.52.0,<0.53.0
on bioconductor-biocgenerics >=0.52.0,<0.53.0a0
on bioconductor-biomart >=2.62.0,<2.63.0
on bioconductor-biomart >=2.62.0,<2.63.0a0
on bioconductor-biostrings >=2.74.0,<2.75.0
on bioconductor-biostrings >=2.74.0,<2.75.0a0
on bioconductor-bsgenome >=1.74.0,<1.75.0
on bioconductor-bsgenome >=1.74.0,<1.75.0a0
on bioconductor-genomicranges >=1.58.0,<1.59.0
on bioconductor-genomicranges >=1.58.0,<1.59.0a0
on bioconductor-iranges >=2.40.0,<2.41.0
on bioconductor-iranges >=2.40.0,<2.41.0a0
on bioconductor-pwalign >=1.2.0,<1.3.0
on bioconductor-pwalign >=1.2.0,<1.3.0a0
on bioconductor-rsamtools >=2.22.0,<2.23.0
on bioconductor-rsamtools >=2.22.0,<2.23.0a0
on bioconductor-s4vectors >=0.44.0,<0.45.0
on bioconductor-s4vectors >=0.44.0,<0.45.0a0
on bioconductor-shortread >=1.64.0,<1.65.0
on bioconductor-shortread >=1.64.0,<1.65.0a0
on bioconductor-summarizedexperiment >=1.36.0,<1.37.0
on bioconductor-summarizedexperiment >=1.36.0,<1.37.0a0
on bioconductor-variantannotation >=1.52.0,<1.53.0
on bioconductor-variantannotation >=1.52.0,<1.53.0a0
on bioconductor-xvector >=0.46.0,<0.47.0
on bioconductor-xvector >=0.46.0,<0.47.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=13
on liblapack >=3.9.0,<4.0a0
on r-base >=4.4,<4.5.0a0
on r-r2html
on r-teachingdemos
on r-xtable

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-r453plus1toolbox

to add into an existing workspace instead, run:

pixi add bioconductor-r453plus1toolbox

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-r453plus1toolbox

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-r453plus1toolbox

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-r453plus1toolbox:<tag>

(see bioconductor-r453plus1toolbox/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-r453plus1toolbox/README.html)