recipe bioconductor-rgntx

Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/RgnTX.html

License:

Artistic-2.0

Recipe:

/bioconductor-rgntx/meta.yaml

RgnTX allows the integration of transcriptome annotations so as to model the complex alternative splicing patterns. It supports the testing of transcriptome elements without clear isoform association, which is often the real scenario due to technical limitations. It involves functions that do permutaion test for evaluating association between features and transcriptome regions.

package bioconductor-rgntx

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-regioner:

>=1.34.0,<1.35.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:

>=3.2.0,<3.3.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

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-rgntx

and update with::

   mamba update bioconductor-rgntx

To create a new environment, run:

mamba create --name myenvname bioconductor-rgntx

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-rgntx:<tag>

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

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