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Getting updates from main before adding more changes for specific assay docs, HTAN index date #16

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merged 6 commits into from
Jun 4, 2024
Merged

Getting updates from main before adding more changes for specific assay docs, HTAN index date #16

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7003a2f
add BQ drs manifest instructions
clarisse-lau May 14, 2024
82cf5fa
Merge pull request #12 from ncihtan/drs-manifest-bq
alexeliotlash May 16, 2024
c586f81
Merge pull request #13 from ncihtan/specific_assay_files
alexeliotlash May 21, 2024
5c7c94b
Added CRC for Harvard
inodb May 23, 2024
8f28b5d
Merge pull request #15 from ncihtan/specific_assay_files
alexeliotlash May 30, 2024
4aedfa7
Merge pull request #14 from ncihtan/add-crc
inodb Jun 3, 2024
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8 changes: 6 additions & 2 deletions access_controlled/CDS_access.md
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Expand Up @@ -16,7 +16,7 @@ To access data via CDS, first generate a CDS Data Repository Service (DRS) manif

1. CDS Portal
2. HTAN Data Portal
3. Google BigQuery (Coming Soon!)
3. Google BigQuery

## 1. Generating a Manifest File from the CDS Portal

Expand Down Expand Up @@ -71,7 +71,11 @@ Click **Download Manifest**, which will download a local file called `cds_manife
![HTAN Portal: Download DRS Manifest](../img/cds_genomics3.png)


## 3. Generating a Manifest File from Google BigQuery (Coming Soon!)
## 3. Generating a Manifest File from Google BigQuery
HTAN metadata and a mapping of HTAN Data File IDs to CDS DRS URIs are available as Google BigQuery tables via the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC) (see [Google BigQuery](https://docs.humantumoratlas.org/open_access/biq_query/)). These tables can be used to subset data to a cohort of interest, and obtain DRS URIs of files to access.

For a step-by-step guide on how to generate a DRS manifest file using Google BigQuery, please see the Python notebook [Creating_CDS_Data_Import_Manifests_Using_BQ.ipynb](https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Creating_CDS_Data_Import_Manifests_Using_BQ.ipynb).



# Accessing Data
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8 changes: 6 additions & 2 deletions open_access/cds_imaging.md
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Expand Up @@ -14,7 +14,7 @@ To access data via CDS, first generate a CDS Data Repository Service (DRS) manif

1. CDS Portal
2. HTAN Data Portal
3. Google BigQuery (Coming Soon!)
3. Google BigQuery

## 1. Generating a Manifest File from the CDS Portal

Expand Down Expand Up @@ -57,7 +57,11 @@ Click **Download Manifest**, which will download a local file called `cds_manife
![HTAN Portal: Download DRS Manifest](../img/cds_img3.png)


## 3. Generating a Manifest File from Google BigQuery (Coming Soon!)
## 3. Generating a Manifest File from Google BigQuery
HTAN metadata and a mapping of HTAN Data File IDs to CDS DRS URIs are available as Google BigQuery tables via the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC) (see [Google BigQuery](https://docs.humantumoratlas.org/open_access/biq_query/)). These tables can be used to subset data to a cohort of interest, and obtain DRS URIs of files to access.

For a step-by-step guide on how to generate a DRS manifest file using Google BigQuery, please see the Python notebook [Creating_CDS_Data_Import_Manifests_Using_BQ.ipynb](https://github.com/isb-cgc/Community-Notebooks/blob/master/HTAN/Python%20Notebooks/Creating_CDS_Data_Import_Manifests_Using_BQ.ipynb).



# Accessing Data
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2 changes: 1 addition & 1 deletion overview/centers.md
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Expand Up @@ -14,7 +14,7 @@ HTAN currently consists of ten research centers, and two pilot projects. There a
| HTA4 | Children’s Hospital of Philadelphia | Tumor Atlas | Pediatric |
| HTA5 | Dana-Farber Cancer Institute | Tumor Atlas | Multiple Cancer Types |
| HTA6 | Duke University | Pre-Cancer Atlas | Breast |
| HTA7 | Harvard Medical School | Pre-Cancer Atlas | Melanoma and Clonal Hematopoiesis |
| HTA7 | Harvard Medical School | Pre-Cancer Atlas | Melanoma, Colorectal Cancer, and Clonal Hematopoiesis |
| HTA8 | Memorial Sloan Kettering Cancer Center | Tumor Atlas | Multiple Cancer Types |
| HTA9 | Oregon Health Science University | Tumor Atlas | Breast |
| HTA10 | Stanford University | Pre-Cancer Atlas | Familial Adenomatous Polyposis |
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