recipe bioconductor-interest

Intron-Exon Retention Estimator

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-interest/meta.yaml

Links:

doi: 10.18129/B9.bioc.IntEREst

This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

package bioconductor-interest

versions:

1.24.0-0,  1.22.2-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1, 

1.24.0-0,  1.22.2-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.6.1-0,  1.4.1-0,  1.2.2-1

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-deseq2:

>=1.40.0,<1.41.0

depends bioconductor-dexseq:

>=1.46.0,<1.47.0

depends bioconductor-edger:

>=3.42.0,<3.43.0

depends bioconductor-genomicalignments:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicfiles:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-seqlogo:

>=1.66.0,<1.67.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dbi:

depends r-rmysql:

depends r-seqinr:

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-interest

and update with::

   mamba update bioconductor-interest

To create a new environment, run:

mamba create --name myenvname bioconductor-interest

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-interest:<tag>

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

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