recipe bioconductor-oder

Optimising the Definition of Expressed Regions

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-oder/meta.yaml

The aim of ODER is to identify previously unannotated expressed regions (ERs) using RNA-sequencing data. For this purpose, ODER defines and optimises the definition of ERs, then connected these ERs to genes using junction data. In this way, ODER improves gene annotation. Gene annotation is a staple input of many bioinformatic pipelines and a more complete gene annotation can enable more accurate interpretation of disease associated variants.

package bioconductor-oder

versions:

1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biocfilecache:

>=2.8.0,<2.9.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-dasper:

>=1.9.0,<1.10.0

depends bioconductor-derfinder:

>=1.34.0,<1.35.0

depends bioconductor-genomeinfodb:

>=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-megadepth:

>=1.10.0,<1.11.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-ggpubr:

depends r-ggrepel:

depends r-magrittr:

depends r-plyr:

depends r-purrr:

depends r-stringr:

depends r-tibble:

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-oder

and update with::

   mamba update bioconductor-oder

To create a new environment, run:

mamba create --name myenvname bioconductor-oder

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-oder:<tag>

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

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