recipe bioconductor-eisar

Exon-Intron Split Analysis (EISA) in R

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/eisaR.html

License:

GPL-3

Recipe:

/bioconductor-eisar/meta.yaml

Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.

package bioconductor-eisar

versions:

1.12.0-0,  1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-edger:

>=3.42.0,<3.43.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-limma:

>=3.56.0,<3.57.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-base:

>=4.3,<4.4.0a0

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-eisar

and update with::

   mamba update bioconductor-eisar

To create a new environment, run:

mamba create --name myenvname bioconductor-eisar

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-eisar:<tag>

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

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