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101 changes: 54 additions & 47 deletions docs/getting_started/index.md
Original file line number Diff line number Diff line change
@@ -1,79 +1,86 @@
---
title: Re-Search made simple
---
# Find the Cancer Data You Need—No Coding Required

<div class="center" markdown> <p>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.</p></div>
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.

!!! 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)*

<div class="grid cards" markdown>
---

- :material-clock-fast:{ .lg .middle } __Don't code? No problem!__
## Choose Your Research Path

---
Whether you prefer a visual interface, cloud-based notebooks, or a full Python environment, the CDA meets you where you are.

Browse through a curated dataset of all subjects that have data at multiple data centers using an intuitive filtering tool right in this website.
<a href="../interactive/" title="interactive search" class="md-button md-button">Head to our interactive page to try it out.
</a></p>
=== "No Code (Interactive)"

- :material-clock-fast:{ .lg .middle } __Low code, no install__
### Explore Data Visually
Perfect for clinical researchers and building cohorts quickly.

* **No Install:** Works entirely in your browser.
* **Intuitive Filtering:** Search by harmonized terms (age, diagnosis, project).
* **Export:** Download your cohort as a `.tsv` to open in Excel.

---
[Try the Interactive Search →](https://cda.readthedocs.io/en/latest/interactive_search.html){ .md-button }

Fill in the blanks in our pre-built queries to find the data you need without installing a thing. <p>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.*<p>
<a href="https://colab.research.google.com/github/CancerDataAggregator/Community-Notebooks/blob/main/Tutorials/Welcome.ipynb" title="Try it now" class="md-button md-button">Launch CDA in the cloud
</a></p>
=== "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.

Check failure

Code scanning / check-spelling

Unrecognized Spelling Error documentation

bioinformaticians is not a recognized word

```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.
<a href="https://colab.research.google.com/github/CancerDataAggregator/Community-Notebooks/blob/main/Tutorials/010_isbcgc.ipynb" title="isbcgcusecase" class="md-button md-button">Test it out on Google Colab
</a></p>

- :simple-swagger:{ .lg .middle } __Developers__

---

Are you building a metadata microservice? Connecting even more databases? Hosting a computational resource? <p>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. |

---

</div>
### Stay Updated
* [Latest Data Releases](https://cda.readthedocs.io/en/latest/)
* [CDA Python Library Updates](https://cda.readthedocs.io/en/latest/release_notes/cdapython_releases.html)

---
[Back to top]
88 changes: 15 additions & 73 deletions docs/index.md
Original file line number Diff line number Diff line change
@@ -1,79 +1,21 @@
---
title: Re-Search made simple
---

<div class="center" markdown> <p>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.</p></div>


<div class="grid cards" markdown>

- :material-clock-fast:{ .lg .middle } __Don't code? No problem!__

---

Browse through a curated dataset of all subjects that have data at multiple data centers using an intuitive filtering tool right in this website.
<a href="interactive/" title="interactive search" class="md-button md-button">Head to our interactive page to try it out.
</a></p>

- :material-clock-fast:{ .lg .middle } __Low code, no install__

---

Fill in the blanks in our pre-built queries to find the data you need without installing a thing. <p>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.*<p>
<a href="https://colab.research.google.com/github/CancerDataAggregator/Community-Notebooks/blob/main/Tutorials/Welcome.ipynb" title="Try it now" class="md-button md-button">Launch CDA in the cloud
</a></p>

- :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.
<a href="https://colab.research.google.com/github/CancerDataAggregator/Community-Notebooks/blob/main/Tutorials/010_isbcgc.ipynb" title="isbcgcusecase" class="md-button md-button">Test it out on Google Colab
</a></p>

- :simple-swagger:{ .lg .middle } __Developers__

---

Are you building a metadata microservice? Connecting even more databases? Hosting a computational resource? <p>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

</div>
| No Code | Low Code | Power Users |
| :--- | :--- | :--- |
| **Interactive Search** | **Cloud Notebooks** | **Python Library** |
| Best for clinical researchers and quick cohort building. | Fill-in-the-blank queries in [FireCloud](https://cda.readthedocs.io/en/latest/) or [CGC](https://cda.readthedocs.io/en/latest/). | Full API access for bioinformatics pipelines and large-scale analysis. |
| [Try it now →](https://cda.readthedocs.io/en/latest/interactive_search.html) | [Launch in Cloud →](https://cda.readthedocs.io/en/latest/#low-code-no-install) | [View API Docs →](https://cda.readthedocs.io/en/latest/developer_tools.html) |

---
2 changes: 1 addition & 1 deletion mkdocs.yml
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remove_input_tags:
- hide_code
include_source: True
execute: True
execute: False
allow_errors: False
ignore: ["documentation/cdapython/vignettes/005_TCIA.ipynb"]

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