With CDA you search by harmonized, common language terms. Using simple language you can get information about the subjects, files, or specimens that you care about in a standard dataframe format (tsv) that you can open in Excel, integrate into a pipeline or upload to your favorite cloud resource.
Send your results to [Broad Institute FireCloud:octicons-link-external-16:](https://datacommons.cancer.gov/analytical-resource/broad-institute-firecloud){:target="_blank"} or [Velsera Cancer Genomics Cloud:octicons-link-external-16:](https://www.cancergenomicscloud.org/){:target="_blank"} for a complete cloud experience. Find the data you need, fetch all the files, and run your favorite bioinformatics pipeline *all without ever leaving your web browser.*
+=== "Low Code (Cloud)" -- :fontawesome-brands-python:{ .lg .middle } __Power users__ + ### Analyze in the Cloud + Fill in the blanks in our pre-built queries to find and process data without local setup. + + * **Connected:** Send results directly to [Broad Institute FireCloud](https://cda.readthedocs.io/en/latest/) or [Velsera Cancer Genomics Cloud](https://cda.readthedocs.io/en/latest/). + * **Scalable:** Run bioinformatics pipelines on the data you find without leaving your browser. - --- + [Launch CDA in the Cloud →](https://cda.readthedocs.io/en/latest/#low-code-no-install){ .md-button } - Install `cdapython` with `pip` and get up - and running in no time +=== "Power Users (Python)" + ### Integrate with Python + For bioinformaticians building automated pipelines. + ```bash - pip3 uninstall -y cdapython; pip3 install git+https://github.com/CancerDataAggregator/cdapython.git@develop - python3 + pip install cdapython ``` ```python - from cdapython import * + from cdapython import Q + # Example: Find subjects with specific diagnosis + r = Q('primary_diagnosis = "Adenocarcinoma"').run() + print(r) ``` -- :fontawesome-brands-python:{ .lg .middle } __Code in the Cloud__ - - --- - - Bring lists of files or subjects found with CDA to the [ISB Cancer Gateway in the Cloud (ISB-CGC):octicons-link-external-16:](https://isb-cgc.org/){:target="_blank"} to instantly access both associated derived data and raw files, for use in cloud processing pipelines -- either in your own preferred environment or using ISB-CGC's free Google Cloud Platform credits program. - Test it out on Google Colab - - -- :simple-swagger:{ .lg .middle } __Developers__ - - --- - - Are you building a metadata microservice? Connecting even more databases? Hosting a computational resource?Whatever your use case, CDA can help. - - [:octicons-arrow-right-24:**API documentation**](../documentation/developers/index.md) + [View Developer Tools →](https://cda.readthedocs.io/en/latest/developer_tools.html){ .md-button } -- :material-bell-alert-outline:{ .lg .middle } __What's new?__ - - --- - - Recently Updated Pages: +--- - - [Data Release](../release_notes/data_updates.md) - - [Code Release](../release_notes/cdapython.md) +## Master the CDA in Minutes -- :simple-mysql:{ .lg .middle } __Need even more data?__ +Check out our video guides to see how the CDA simplifies complex data cross-referencing. - --- +* [📺 Video: Intro to CDA](https://cda.readthedocs.io/en/latest/vignettes/video_intro.html) +* [📺 Video: Build a Cohort Interactively](https://cda.readthedocs.io/en/latest/vignettes/video_build_a_cohort_interactively.html) +* [📺 Video: Cohort Building with Python](https://cda.readthedocs.io/en/latest/vignettes/video_cohort_building_with_cdapython.html) - Do you dream of having a CDA database instance of your very own? Or CDA but bigger somehow? - We can make those dreams come true. Let's chat! +--- - :material-email: cancerdataaggregator `@` gmail +## Why Use the CDA? +| Feature | The CDA Advantage | +| :--- | :--- | +| **Harmonization** | We translate different data center terms into one common language. | +| **Cross-Center** | Find subjects that have data in GDC, PDC, and IDC simultaneously. | +| **Versatility** | Move from a simple search to a massive cloud pipeline in the same ecosystem. | +--- -
With CDA you search by harmonized, common language terms. Using simple language you can get information about the subjects, files, or specimens that you care about in a standard dataframe format (tsv) that you can open in Excel, integrate into a pipeline or upload to your favorite cloud resource.
Send your results to [Broad Institute FireCloud:octicons-link-external-16:](https://datacommons.cancer.gov/analytical-resource/broad-institute-firecloud){:target="_blank"} or [Velsera Cancer Genomics Cloud:octicons-link-external-16:](https://www.cancergenomicscloud.org/){:target="_blank"} for a complete cloud experience. Find the data you need, fetch all the files, and run your favorite bioinformatics pipeline *all without ever leaving your web browser.*
- -- :fontawesome-brands-python:{ .lg .middle } __Power users__ - - --- - - Install `cdapython` with `pip` and get up - and running in no time - - ```bash - pip3 uninstall -y cdapython; pip3 install git+https://github.com/CancerDataAggregator/cdapython.git@develop - python3 - ``` +# Find the Cancer Data You Need—No Coding Required - ```python - from cdapython import * - ``` +The **Cancer Data Aggregator (CDA)** connects you to subjects, files, and specimens across **GDC**, **PDC**, and **IDC** through one simple interface. Filter by common clinical terms and export results directly to Excel or the Cloud. -- :fontawesome-brands-python:{ .lg .middle } __Code in the Cloud__ - - --- - - Bring lists of files or subjects found with CDA to the [ISB Cancer Gateway in the Cloud (ISB-CGC):octicons-link-external-16:](https://isb-cgc.org/){:target="_blank"} to instantly access both associated derived data and raw files, for use in cloud processing pipelines -- either in your own preferred environment or using ISB-CGC's free Google Cloud Platform credits program. - Test it out on Google Colab - - -- :simple-swagger:{ .lg .middle } __Developers__ - - --- - - Are you building a metadata microservice? Connecting even more databases? Hosting a computational resource?Whatever your use case, CDA can help. - - [:octicons-arrow-right-24:**API documentation**](documentation/developers/) - -- :material-bell-alert-outline:{ .lg .middle } __What's new?__ - - --- - - Recently Updated Pages: - - - [Data Release](release_notes/data_updates.md) - - [Code Release](release_notes/cdapython.md) - -- :simple-mysql:{ .lg .middle } __Need even more data?__ - - --- - - Do you dream of having a CDA database instance of your very own? Or CDA but bigger somehow? - We can make those dreams come true. Let's chat! - - :material-email: cancerdataaggregator `@` gmail +!!! abstract "Start Here" + If you want to browse data visually without writing any code, our interactive tool is the best place to begin. + + [🚀 Start Searching Interactively](https://cda.readthedocs.io/en/latest/interactive_search.html){ .md-button .md-button--primary } + *(No installation or account needed)* +--- +### Three Ways to Access Data -