recipe bioconductor-r453plus1toolbox

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

Homepage:

https://bioconductor.org/packages/3.17/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:

1.50.0-0,  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, 

1.50.0-0,  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 bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biomart:

>=2.56.0,<2.57.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-bsgenome:

>=1.68.0,<1.69.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-shortread:

>=1.58.0,<1.59.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

depends bioconductor-xvector:

>=0.40.0,<0.41.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-r2html:

depends r-teachingdemos:

depends r-xtable:

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-r453plus1toolbox

and update with::

   mamba update bioconductor-r453plus1toolbox

To create a new environment, run:

mamba create --name myenvname bioconductor-r453plus1toolbox

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-r453plus1toolbox:<tag>

(see `bioconductor-r453plus1toolbox/tags`_ for valid values for ``<tag>``)

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