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Welcome to St. Jude Cloud Documentation!

Overview

Here, you'll find the authoritative guides for accessing St. Jude Cloud data, running analysis workflows (ours or your own) on the cloud, and exploring curated data from numerous published studies by St. Jude and our collaborating institutions. For a brief overview of everything St. Jude Cloud provides, we recommend that you watch the video on our home page.

Sign up here to receive email notifications when we add new datasets, analysis pipelines, or other exciting features.

Features

You can leverage many different capabilities of St. Jude Cloud in your research, such as:

  • Explore the raw genomics data we currently offer. You can browse by diagnosis, publication, or curated dataset while applying a number of different filters. For more information, see our data request guide.
  • Run your tools on our data by requesting data and packaging your tools in a secure cloud environment. See this guide for an example.
  • Run our in house analysis workflows on your data by moving your data to the cloud and selecting a workflow to run. See this guide for an example.
  • Explore St. Jude datasets through interactive visualizations that we have packaged for the community. For example, visit PeCan to visually investigate pediatric cancer mutation data.
  • Create manuscript quality figures with your data for use in publications or to host on your website with ProteinPaint or GenomePaint. See the ProteinPaint and GenomePaint doc pages for help.

Note

Please note that while it is free to receive and store our data in St. Jude Cloud, there are compute and storage fees associated with working in the cloud, as well as egress fees for downloading our data.

Datasets

The following projects currently distribute their data through St. Jude Cloud. Click here for more information about the projects listed below.

  • Pediatric Cancer Genome Project (PCGP)
  • St. Jude Lifetime (SJLIFE)
  • Clinical Genomics (Clinical Pilot and G4K)
  • Sickle Cell Genome Project (SGP)
  • Childhood Cancer Survivor Study (CCSS)

Analysis Workflows

St. Jude shares a number of end-to-end analysis workflows on the cloud. Click on the links below to learn more about the workflow.

Portals

St. Jude Cloud provides a number of user portals which you can use to interactively explore the results we produce. Click on the links below to visit each of the corresponding portals.

  • Pediatric Cancer Portal (PeCan). Interactively explore mutational recurrence and pathogenicity assessment of variants in pediatric cancer using a wide variety of St. Jude + publicly available data.
  • Sickle Cell Diseases Portal. Explore the latest from the Sickle Cell Genomics Project (a collaboration between St. Jude and Baylor College of Medicine).

Citing St. Jude Cloud

We are currently in progress of preparing a paper for St. Jude Cloud.

Until further notice, please cite the relevant paper for each of the datasets and/or resources below that you used in your study.

St. Jude Cloud Resource Citation
Pediatric Cancer Genome Project (PCGP) dataset PCGP perspectives paper and the relevant tumor type paper(s)
St. Jude Lifetime (SJLIFE) dataset SJLIFE paper
Clinical Pilot (non-G4K clinical genomics) dataset Clinical Pilot paper
Genomes for Kids (G4K) dataset paper in progress
Sickle Cell Genome Project (SGP) dataset paper in progress
Childhood Cancer Survivor Study (CCSS) dataset CCSS study design paper
ProteinPaint ProteinPaint paper
GenomePaint paper in progress
PeCan Pie PeCan Pie paper
NeoepitopePred NeoepitopePred paper
ChIP-Seq Peak Calling unpublished
Rapid RNA-Seq Fusion Detection paper in progress
WARDEN unpublished
Mutational Signatures Mutational Patterns paper
cis-x paper in progress

Note

If you are unsure what datasets the data that you have been vended belongs to, you can find this information in the sj_datasets column of the SAMPLE_INFO.txt file.

Warning

Publishing using any of the data files before the embargo date has passed is strictly prohibited as outlined in the Data Access Agreement (DAA).

Contact Us

Any questions, comments, or concerns can be directed to our "Contact Us" form or you can email us directly at support@stjude.cloud.