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:

1.6.0-0,  1.2.0-0

Depends:

  • on bioconductor-biocparallel >=1.44.0,<1.45.0

  • on bioconductor-complexheatmap >=2.26.0,<2.27.0

  • on bioconductor-deseq2 >=1.50.0,<1.51.0

  • on bioconductor-summarizedexperiment >=1.40.0,<1.41.0

  • on r-base >=4.5,<4.6.0a0

  • on r-ggplot2

  • on r-patchwork

  • on r-rcolorbrewer

  • on r-rlang

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-hybridexpress

to add into an existing workspace instead, run:

pixi add bioconductor-hybridexpress

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-hybridexpress

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-hybridexpress

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-hybridexpress:<tag>

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-hybridexpress/README.html)