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4 Uploading a Trio to Curated Trio Datasets

BenchHub Team

2026-01-28

Source: vignettes/v04_uploading_a_Trio.rmd
v04_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 sheet. Curated Trio Dataset is a list of datasets with proven utility. 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, supporting evidence, 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 supporting evidence 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 supporting evidence 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 supporting evidence).
    • 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!

Session Info 

## R version 4.5.2 (2025-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
## 
## time zone: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.38.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.39       desc_1.4.3          R6_2.6.1           
##  [4] bookdown_0.46       fastmap_1.2.0       xfun_0.56          
##  [7] cachem_1.1.0        knitr_1.51          htmltools_0.5.9    
## [10] rmarkdown_2.30      lifecycle_1.0.5     cli_3.6.5          
## [13] sass_0.4.10         pkgdown_2.2.0       textshaping_1.0.4  
## [16] jquerylib_0.1.4     systemfonts_1.3.1   compiler_4.5.2     
## [19] tools_4.5.2         ragg_1.5.0          bslib_0.10.0       
## [22] evaluate_1.0.5      yaml_2.3.12         BiocManager_1.30.27
## [25] jsonlite_2.0.0      rlang_1.1.7         fs_1.6.6           
## [28] htmlwidgets_1.6.4