- recipe bioconductor-cosia
An Investigation Across Different Species and Tissues
- Homepage:
- License:
MIT + file LICENSE
- Recipe:
Cross-Species Investigation and Analysis (CoSIA) is a package that provides researchers with an alternative methodology for comparing across species and tissues using normal wild-type RNA-Seq Gene Expression data from Bgee. Using RNA-Seq Gene Expression data, CoSIA provides multiple visualization tools to explore the transcriptome diversity and variation across genes, tissues, and species. CoSIA uses the Coefficient of Variation and Shannon Entropy and Specificity to calculate transcriptome diversity and variation. CoSIA also provides additional conversion tools and utilities to provide a streamlined methodology for cross-species comparison.
- package bioconductor-cosia¶
- versions:
1.2.0-0,1.0.0-0- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-annotationtools:
>=1.76.0,<1.77.0- depends bioconductor-biomart:
>=2.58.0,<2.59.0- depends bioconductor-experimenthub:
>=2.10.0,<2.11.0- depends bioconductor-org.ce.eg.db:
>=3.18.0,<3.19.0- depends bioconductor-org.dm.eg.db:
>=3.18.0,<3.19.0- depends bioconductor-org.dr.eg.db:
>=3.18.0,<3.19.0- depends bioconductor-org.hs.eg.db:
>=3.18.0,<3.19.0- depends bioconductor-org.mm.eg.db:
>=3.18.0,<3.19.0- depends bioconductor-org.rn.eg.db:
>=3.18.0,<3.19.0- depends r-base:
>=4.3,<4.4.0a0- depends r-dplyr:
>=1.0.7- depends r-ggplot2:
>=3.3.5- depends r-homologene:
>=1.4.68.19- depends r-magrittr:
>=2.0.1- depends r-plotly:
>=4.10.0- depends r-rcolorbrewer:
>=1.1-2- depends r-readr:
>=2.1.1- depends r-stringr:
>=1.4.0- depends r-tibble:
>=3.1.7- depends r-tidyr:
>=1.2.0- depends r-tidyselect:
>=1.1.2- 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-cosia and update with:: mamba update bioconductor-cosia
To create a new environment, run:
mamba create --name myenvname bioconductor-cosia
with
myenvnamebeing 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-cosia:<tag> (see `bioconductor-cosia/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-cosia/README.html)
