recipe bioconductor-generxcluster

gRx Differential Clustering

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-generxcluster/meta.yaml

Links:

biotools: generxcluster

Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here.

package bioconductor-generxcluster

(downloads) docker_bioconductor-generxcluster

Versions:
1.46.0-0,  1.42.0-0,  1.38.0-0,  1.36.0-0,  1.34.0-1,  1.34.0-0,  1.30.0-2,  1.30.0-1,  1.30.0-0, 

1.46.0-0,  1.42.0-0,  1.38.0-0,  1.36.0-0,  1.34.0-1,  1.34.0-0,  1.30.0-2,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0

Depends:

  • on bioconductor-genomicranges >=1.62.0,<1.63.0

  • on bioconductor-genomicranges >=1.62.1,<1.63.0a0

  • on bioconductor-iranges >=2.44.0,<2.45.0

  • on bioconductor-iranges >=2.44.0,<2.45.0a0

  • on libblas >=3.9.0,<4.0a0

  • on libgcc >=14

  • on liblapack >=3.9.0,<4.0a0

  • on liblzma >=5.8.2,<6.0a0

  • on libzlib >=1.3.1,<2.0a0

  • 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-generxcluster

to add into an existing workspace instead, run:

pixi add bioconductor-generxcluster

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-generxcluster

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-generxcluster

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-generxcluster:<tag>

(see bioconductor-generxcluster/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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