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Add gget CLI client to docs (#11035)
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* Add gget CLI client to docs

* add maintainers

* fix typos
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inodb authored Nov 22, 2024
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15 changes: 13 additions & 2 deletions docs/web-API-and-Clients.md
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Expand Up @@ -13,6 +13,7 @@ The cBioPortal REST API is described using Swagger/OpenAPI, which allows one to
There are multiple ways to access the API using R. Below are two recommended R packages to access cBioPortal data.

#### cBioPortalData (recommended)
*Maintainer: [Marcel Ramos Pérez](https://github.com/LiNk-NY), [Levi Waldron](https://github.com/lwaldron)*

cBioPortalData aims to import all cBioPortal datasets as MultiAssayExperiment objects in Bioconductor. Some of its key features:

Expand All @@ -35,6 +36,7 @@ cBioPortal(
```

#### cbioportalR (recommended)
*Maintainer: [Karissa Whiting](https://github.com/karissawhiting)*

cbioportalR offers easy-to-use functions that allow users to browse and pull data from public or institutional cBioPortal sites without knowledge of web service or Bioconductor infrastructures. The package is tidyverse-compatible. Key package features include:

Expand All @@ -48,6 +50,7 @@ cbioportalR offers easy-to-use functions that allow users to browse and pull dat
For a detailed tutorial on `cbioportalR`, see the package website: https://www.karissawhiting.com/cbioportalR/articles/overview-of-workflow.html

#### rapiclient
*Maintainer: [Darko Bergant](https://github.com/bergant), [Marcel Ramos Pérez](https://github.com/LiNk-NY)*

Although we recommend [cBioPortalData](/#cbioportaldata-recommended) or [cbioportalR](/#cbioportalR-recommended) for most use cases, it is possible to connect to the API directly using [rapiclient](https://github.com/bergant/rapiclient):

Expand All @@ -56,15 +59,16 @@ library(rapiclient)
client <- get_api(url = "https://www.cbioportal.org/api/v2/api-docs")
```

#### CGDSR (will be deprecated)
#### CGDSR (deprecated)

The CGDS-R package connects an older version of our web API (`webservice.do`). Althought we will continue to keep `webservice.do` running for a while, we can't guarantee the same level of quality as our new API (`cbioportal.org/api`) provides. Therefore we recommend that you use `cBioPortalData` instead.
The CGDS-R package connected to an older version of our web API (`webservice.do`). We no longer support this API and recommend people switch to our new API (`cbioportal.org/api`) by migrating to one of the other R clients instead.

### Python client

There are multiple ways to access the API using Python. One can use the `bravado` package to access the API directly, or use the `cbio_py` client, which provides a simple wrapper for the API and returns data in a format that is easy to work with.

#### bravado
*Maintainer: Yelp*

Generate a client in Python using [bravado](https://github.com/Yelp/bravado) like this:

Expand Down Expand Up @@ -135,5 +139,12 @@ cbioportal = SwaggerClient.from_url('https://genie.cbioportal.org/api/v2/api-doc
A Jupyter notebook with more examples can be found [here](https://github.com/mskcc/cbsp-hackathon/blob/master/0-introduction/cbsp\_hackathon.ipynb).

#### cbio\_py
*Maintainer: [Sasha Dagayev](https://www.linkedin.com/in/sasha-dagayev/)*

See the `cbio_py` documentation: https://pypi.org/project/cbio-py/.


#### gget
*Maintainer: [Sam Wagenaar](https://github.com/techno-sam)*

Plot cancer genomics heatmaps using data from cBioPortal using Ensembl IDs or gene names. See: https://pachterlab.github.io/gget/en/cbio.html. The `gget` client is also a command line client, providing access to many other bioinformatics resources beyond cBioPortal.

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