https://github.com/uclouvain-cbio/depmap
Cancer Dependency Map package
https://github.com/uclouvain-cbio/depmap
bioconductor bioconductor-package depmap
Last synced: 8 months ago
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Cancer Dependency Map package
- Host: GitHub
- URL: https://github.com/uclouvain-cbio/depmap
- Owner: UCLouvain-CBIO
- Created: 2019-02-08T09:54:18.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-08-16T08:35:24.000Z (almost 2 years ago)
- Last Synced: 2024-08-16T16:47:56.096Z (almost 2 years ago)
- Topics: bioconductor, bioconductor-package, depmap
- Language: R
- Homepage: https://uclouvain-cbio.github.io/depmap/
- Size: 1.48 GB
- Stars: 24
- Watchers: 3
- Forks: 8
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# The `depmap` package
## Introduction
[depmap](https://github.com/UCLouvain-CBIO/depmap/) is an
R/Bioconductor data package that disseminates cancer dependency omics
datasets from the [Broad Institute
depmap](https://depmap.org/portal/download/) project.
- Portal: https://depmap.org/portal/
- Selected publications: see https://depmap.org/portal/depmap/
The [github page](https://github.com/UCLouvain-CBIO/depmap) page is
for active development, issue tracking and forking/pulling purposes.
The [depmap](https://github.com/UCLouvain-CBIO/depmap/) package aims
to provide a reproducible research framework to cancer dependency data
described by [Tsherniak, Aviad, et al. "Defining a cancer dependency
map." Cell 170.3 (2017):
564-576.](https://www.ncbi.nlm.nih.gov/pubmed/28753430).
To get an overview of the package, see the depmap vignette.
## Installation
To install [depmap](https://github.com/UCLouvain-CBIO/depmap/), the
[BiocManager](https://cran.r-project.org/web/packages/BiocManager/index.html)
Bioconductor Project Package Manager is required. If
[BiocManager](https://cran.r-project.org/web/packages/BiocManager/index.html)
is not already installed, it will need to be done so beforehand with
(within R) `install.packages("BiocManager")`. Once it is installed,
`depmap` can be installed from Biocondctor:
```r
install.packages("BiocManager")
BiocManager::install("depmap")
```
To install the version from GitHub, use
```r
install.packages("BiocManager")
BiocManager::install("UCLouvain-CBIO/depmap")
```
## Questions
Feel also free to open a GitHub
[issue](https://github.com/UCLouvain-CBIO/depmap/issues), in
particular for bug reports.
Questions can also be posted on the [Bioconductor
forum](https://support.bioconductor.org/).
## Contributing
Contributions to the package are more than welcome. If you want to
contribute to this package, you should follow the same conventions as
the rest of the functions. Please do get in touch (preferable opening
a [github issue](https://github.com/UCLouvain-CBIO/depmap/issues/)) to
discuss any suggestions.
Please note that this project is released with a [Contributor Code of
Conduct](https://github.com/UCLouvain-CBIO/depmap/blob/master/CONDUCT.md).
By participating in this project you agree to abide by its terms.