recipe bioconductor-generegionscan

GeneRegionScan

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-generegionscan/meta.yaml

Links:

biotools: generegionscan

A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.

package bioconductor-generegionscan

(downloads) docker_bioconductor-generegionscan

Versions:
1.66.0-0,  1.62.0-0,  1.58.0-0,  1.56.0-0,  1.54.0-0,  1.50.0-0,  1.48.0-0,  1.46.0-1,  1.46.0-0, 

1.66.0-0,  1.62.0-0,  1.58.0-0,  1.56.0-0,  1.54.0-0,  1.50.0-0,  1.48.0-0,  1.46.0-1,  1.46.0-0,  1.44.0-0,  1.42.0-0,  1.40.0-1,  1.38.0-0,  1.36.0-0,  1.34.0-0

Depends:

  • on bioconductor-affxparser >=1.82.0,<1.83.0

  • on bioconductor-biobase >=2.70.0,<2.71.0

  • on bioconductor-biostrings >=2.78.0,<2.79.0

  • on bioconductor-s4vectors >=0.48.0,<0.49.0

  • on r-base >=4.5,<4.6.0a0

  • on r-rcolorbrewer

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-generegionscan

to add into an existing workspace instead, run:

pixi add bioconductor-generegionscan

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-generegionscan

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-generegionscan

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-generegionscan:<tag>

(see bioconductor-generegionscan/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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