recipe bioconductor-bbcanalyzer

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/BBCAnalyzer.html

License:

LGPL-3

Recipe:

/bioconductor-bbcanalyzer/meta.yaml

Links:

biotools: bbcanalyzer, doi: 10.1186/s12859-017-1549-4

BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.

package bioconductor-bbcanalyzer

(downloads) docker_bioconductor-bbcanalyzer

Versions:
1.40.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0, 

1.40.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-0

Depends:

  • on bioconductor-biostrings >=2.78.0,<2.79.0

  • on bioconductor-genomicranges >=1.62.0,<1.63.0

  • on bioconductor-iranges >=2.44.0,<2.45.0

  • on bioconductor-rsamtools >=2.26.0,<2.27.0

  • on bioconductor-summarizedexperiment >=1.40.0,<1.41.0

  • on bioconductor-variantannotation >=1.56.0,<1.57.0

  • on r-base >=4.5,<4.6.0a0

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-bbcanalyzer

to add into an existing workspace instead, run:

pixi add bioconductor-bbcanalyzer

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-bbcanalyzer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-bbcanalyzer

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-bbcanalyzer:<tag>

(see bioconductor-bbcanalyzer/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.

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Render an install-with-bioconda 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-bbcanalyzer/README.html)