recipe bioconductor-hybridexpress

Comparative analysis of RNA-seq data for hybrids and their progenitors

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-hybridexpress/meta.yaml

HybridExpress can be used to perform comparative transcriptomics analysis of hybrids (or allopolyploids) relative to their progenitor species. The package features functions to perform exploratory analyses of sample grouping, identify differentially expressed genes in hybrids relative to their progenitors, classify genes in expression categories (N = 12) and classes (N = 5), and perform functional analyses. We also provide users with graphical functions for the seamless creation of publication-ready figures that are commonly used in the literature.

package bioconductor-hybridexpress

(downloads) docker_bioconductor-hybridexpress

versions:

1.2.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-complexheatmap:

>=2.22.0,<2.23.0

depends bioconductor-deseq2:

>=1.46.0,<1.47.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

depends r-patchwork:

depends r-rcolorbrewer:

depends r-rlang:

requirements:

additional platforms:

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-hybridexpress

and update with::

   mamba update bioconductor-hybridexpress

To create a new environment, run:

mamba create --name myenvname bioconductor-hybridexpress

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-hybridexpress:<tag>

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

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