- 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:
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¶
- 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>``)
Download stats¶
Link to this page¶
Render an 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)