Helpful tips

How to get dbGaP Access?

How to get dbGaP Access?

To obtain dbGaP access, navigate to the eRA Commons Access site. Learn about eRA Commons and how to register an organization or institution, as well as how to obtain an eRA Commons account at the eRA Commons Frequently Asked Questions (FAQ) site.

What is controlled access data?

Controlled Data The Controlled Access tier includes information which is unique to an individual. This includes most raw data files, and some processed data such as: Primary sequencing data (BAM and FASTQ files) from DNA, RNA, miRNA or bisulfite sequencing studies. Raw and processed SNP6 array data.

How do I submit dbGaP?

To fill out the study config, go to your study’s dbGaP Submission Portal ( Click on “Create” if newly filling out the study config or click on “Edit” to modify an existing study config. Once done, press “Submit” and you will be taken back to the study’s Submission Portal page.

How do I get access to Tcga?

Popular Answers (1)

  1. Connect to
  2. Select the cancer subtype you are interested in (i.e breast invasive carcinoma)
  3. Select mRNA.
  4. Now you can see a table where rows are representing different patients.

How do I download data from dbGaP?

Visit dbGaP, click on Controlled Access Data , then login with your eRA Commons account. You’ll see the dataset previously applied for and approved under the tab Authorized Access -> My Requests . In the column Actions click Request Files for the dataset you want to download.

What is DB gap?

Database of Genotype and Phenotype (dbGaP) refers to NIH maintained database of datasets and was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. dbGaP provides two types of data – open access and controlled access.

How do I download clinical data from TCGA?

Just go to homepage , see the list of studies, in front of which there will be an option for view genomic/clinical data (icon is red color pie chart), just click that, it opens all the data features (you can further explore ). Just download from the option on the upper right (Download clinical data).

How do I open geo datasets?

Once on the GEO website there are multiple different options for searching datasets. The most straight-forward method can be found by clicking on ‘Datasets’ under the ‘Browse Content’ column. The ‘Datasets’ link will open the GEO Dataset Browser; click on ‘Advanced Search’.

What are the terms of use for dbGaP request?

Submission of the data access request will constitute agreement and acknowledgment by both the PI and the SO to the terms of use for the specific dataset(s) requested, which are detailed in the accompanying “Data Use Certification” (DUC) documents that are provided on the website.

How to obtain dbGaP access to controlled data?

To obtain dbGaP access, navigate to the dbGaP Authorized Access site and follow the instructions. A list of other helpful links to learn more about the dbGaP process include: If playback doesn’t begin shortly, try restarting your device. Full screen is unavailable. Learn More

How to request access to individual level data?

In order to request access to any of the individual-level datasets within the controlled-access portions of the database, the Principal Investigator (PI) and the Signing Official (SO) at the investigator’s institution will need to co-sign a request for data access, which will be reviewed by an NIH Data Access Committee at the appropriate NIH

What is the database of genotypes and Phenotypes ( dbGaP )?

dbGaP The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans.