- recipe bioconductor-depmap
Cancer Dependency Map Data Package
- Homepage:
https://bioconductor.org/packages/3.20/data/experiment/html/depmap.html
- License:
Artistic-2.0
- Recipe:
The depmap package is a data package that accesses datsets from the Broad Institute DepMap cancer dependency study using ExperimentHub. Datasets from the most current release are available, including RNAI and CRISPR-Cas9 gene knockout screens quantifying the genetic dependency for select cancer cell lines. Additional datasets are also available pertaining to the log copy number of genes for select cell lines, protein expression of cell lines as measured by reverse phase protein lysate microarray (RPPA), 'Transcript Per Million' (TPM) data, as well as supplementary datasets which contain metadata and mutation calls for the other datasets found in the current release. The 19Q3 release adds the drug_dependency dataset, that contains cancer cell line dependency data with respect to drug and drug-candidate compounds. The 20Q2 release adds the proteomic dataset that contains quantitative profiling of proteins via mass spectrometry. This package will be updated on a quarterly basis to incorporate the latest Broad Institute DepMap Public cancer dependency datasets. All data made available in this package was generated by the Broad Institute DepMap for research purposes and not intended for clinical use. This data is distributed under the Creative Commons license (Attribution 4.0 International (CC BY 4.0)).
- package bioconductor-depmap¶
- Versions:
1.24.0-0,1.20.0-0,1.16.0-0,1.14.0-0,1.12.0-0,1.8.0-1,1.8.0-0,1.6.0-0,1.4.0-1,1.24.0-0,1.20.0-0,1.16.0-0,1.14.0-0,1.12.0-0,1.8.0-1,1.8.0-0,1.6.0-0,1.4.0-1,1.4.0-0,1.2.0-0,1.0.0-0- Depends:
on bioconductor-annotationhub
>=4.0.0,<4.1.0on bioconductor-biocfilecache
>=3.0.0,<3.1.0on bioconductor-data-packages
>=20260207on bioconductor-experimenthub
>=3.0.0,<3.1.0on curl
on r-base
>=4.5,<4.6.0a0on r-curl
on r-dplyr
on r-httr2
on r-tibble
- 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-depmap
to add into an existing workspace instead, run:
pixi add bioconductor-depmap
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-depmap
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-depmap
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-depmap:<tag>
(see bioconductor-depmap/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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-depmap/README.html)
