- recipe bioconductor-octad
Open Cancer TherApeutic Discovery (OCTAD)
- Homepage:
- License:
Artistic-2.0
- Recipe:
OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene expression signature of disease by tamping down over-expressed genes and stimulating weakly expressed ones. The package offers deep-learning based reference tissue selection, disease gene expression signature creation, pathway enrichment analysis, drug reversal potency scoring, cancer cell line selection, drug enrichment analysis and in silico hit validation. It currently covers ~20,000 patient tissue samples covering 50 cancer types, and expression profiles for ~12,000 distinct compounds.
- package bioconductor-octad¶
- versions:
1.4.0-0,1.2.0-0,1.0.0-0- depends bioconductor-annotationhub:
>=3.10.0,<3.11.0- depends bioconductor-biobase:
>=2.62.0,<2.63.0- depends bioconductor-deseq2:
>=1.42.0,<1.43.0- depends bioconductor-edaseq:
>=2.36.0,<2.37.0- depends bioconductor-edger:
>=4.0.0,<4.1.0- depends bioconductor-experimenthub:
>=2.10.0,<2.11.0- depends bioconductor-gsva:
>=1.50.0,<1.51.0- depends bioconductor-limma:
>=3.58.0,<3.59.0- depends bioconductor-octad.db:
>=1.4.0,<1.5.0- depends bioconductor-rhdf5:
>=2.46.0,<2.47.0- depends bioconductor-ruvseq:
>=1.36.0,<1.37.0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends r-base:
>=4.3,<4.4.0a0- depends r-data.table:
- depends r-dplyr:
- depends r-foreach:
- depends r-ggplot2:
- depends r-htmlwidgets:
- depends r-httr:
- depends r-magrittr:
- depends r-plotly:
- depends r-reshape2:
- depends r-rfast:
- 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-octad and update with:: mamba update bioconductor-octad
To create a new environment, run:
mamba create --name myenvname bioconductor-octad
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-octad:<tag> (see `bioconductor-octad/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-octad/README.html)
