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Uploading a Trio to Curated Trio Datasets

BenchHub Team

2025-05-15

Source: vignettes/WIP/Uploading_a_Trio.rmd
Uploading_a_Trio.rmd

Instructions for Uploading a Trio to Curated Trio Datasets

This guide provides step-by-step instructions for uploading a Trio object to the Curated Trio Datasets. It includes creating a GitHub Personal Access Token (PAT) with gist write access and uploading data to Figshare.

Step 1: Create a GitHub Personal Access Token (PAT)

To upload metrics as a GitHub Gist, you need a GitHub PAT with gist write access.

  1. Log in to your GitHub account.
  2. Navigate to Settings > Developer settings > Personal access tokens > Tokens (classic).
  3. Click Generate new token.
  4. Select the following scopes:
    • gist (for creating and managing gists)
  5. Click Generate token and copy the token.

Set the PAT in R

Add the token to your environment in R:

Sys.setenv(GITHUB_PAT = "your_personal_access_token")

Replace "your_personal_access_token" with the token you copied.

Ensure googlesheets4 is set up

  1. Install the googlesheets4 package if you haven’t already:

    install.packages("googlesheets4")

  2. Authenticate with your Google account:

    googlesheets4::gs4_auth()

Step 2: Add the Trio to Curated Trio Datasets

  1. In R, create a Trio object and ensure it is properly populated with data, auxiliary data, and metrics.
  2. Use the writeCTD() method to upload the Trio metadata to the Curated Trio Datasets sheet:
trio$writeCTD(name = "Your Dataset Name")
  1. Follow the prompts to:
    • Save the dataset and auxiliary data locally (optional).
    • Provide the Figshare URL. For more detailed instructions on uploading to Figshare, see below.
    • Select the data type (e.g., omics, clinical, spatial, other).
    • Confirm the upload of auxiliary data to Figshare.

Step 3: Verify the Upload

  1. Check the Curated Trio Datasets Google Sheet to ensure your dataset has been added: Curated Trio Datasets

  2. Verify that the metrics have been uploaded as a GitHub Gist.

Notes

  • Ensure you have an active internet connection during the upload process.
  • If you encounter any issues, check that your GitHub PAT and Figshare URL are correctly set.

Uploading Data to Figshare

  1. Log in to your Figshare account.
  2. Click Create a new item.
  3. Fill in the required metadata fields (e.g., title, description, tags).
  4. Upload your dataset files (e.g., .rds files for the dataset and auxiliary data).
    • NOTE: writeCTD can create the
  5. Publish the item to make it publicly accessible.
  6. Copy the Figshare URL of the published item.

Happy uploading!