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Update web-API-and-Clients.md #10209

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19 changes: 16 additions & 3 deletions docs/web-API-and-Clients.md
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Expand Up @@ -8,9 +8,9 @@ Please see the full reference documentation for the API [here](https://www.cbiop

The cBioPortal REST API is described using Swagger/OpenAPI, which allows one to generate a client in most programming languages. One can use the command line tool `curl` for dowloading data on the command line or use another language such as `Python` or `R` to make visualizations. We list some common examples below, but if your language is not listed, there is likely a client generator available elsewhere (see e.g. https://swagger.io/tools/swagger-codegen/). Do reach out if you'd like us to add a language.

### R client
### R clients

There are multiple ways to access the API using R. The recommended way is to use `cBioPortalData`.
There are multiple ways to access the API using R. Below are two recommended R packages to access cBioPortal data.

#### cBioPortalData (recommended)

Expand All @@ -34,9 +34,22 @@ cBioPortal(
)
```

#### cbioportalR (recommended)

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:

1. Comprehensive documentation aimed at helping clinical researchers understand the underlying structure of cBioPortal data
2. [Tutorials]([https://www.karissawhiting.com/cbioportalR/articles/overview-of-workflow.html]) for quick API authentication and set up
3. Functions to pull complete clinical and genomic data by study ID, molecular profile ID, sample list IDs or individual sample ID (e.g. `get_genetics_by_study()`, `get_genetics_by_sample()`)
4. Functions to navigate and identify patient IDs, sample IDs or study IDs as needed, or infer necessary ID information for queries when not supplied by user.
5. Helper functions to pull information on gene panels (`get_gene_panel()`), or lookup entrez ID (`get_entrez_id()`), Hugo Symbol (`get_hugo_symbol()`) or common gene aliases (`get_alias()`) of genes
6. Capability to query multiple sample IDs from different studies concurrently

For a detailed tutorial on `cbioportalR`, see the package website: https://www.karissawhiting.com/cbioportalR/articles/overview-of-workflow.html

#### rapiclient

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

```
library(rapiclient)
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