Welcome to St. Jude Cloud Documentation!
Here, you'll find authoritative guides for accessing St. Jude Cloud data, running analysis workflows (our workflows 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.
You can apply many different capabilities of St. Jude Cloud to 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 to use in publications or to host on your website with ProteinPaint or GenomePaint. See the ProteinPaint and GenomePaint doc pages for help.
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.
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)
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.
- PeCan Pie
- ChIP-Seq Peak Calling
- Rapid RNA-Seq Fusion Detection
- WARDEN Differential Expression Analysis
- Mutational Signatures
- cis-x (coming soon)
- XenoCP (coming soon)
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 the St. Jude Cloud manuscript. Until further notice, please ensure that when St. Jude Cloud or data accessed therein is used in your work, please:
Cite the relevant paper for each of the datasets and/or resources (see table below) that you used in your study.
State in the Results and/or Methods section that the relevant data was obtained from St. Jude Cloud. Example statement:
"Whole genome sequencing data for relapse tumor samples from 345 pediatric patients were obtained from St. Jude Cloud."
State in the Data availability section of the manuscript that data can be accessed via St. Jude Cloud. Example statement:
"Whole genome sequencing data for pediatric relapse tumor samples used for analysis in this study were obtained from St. Jude Cloud (https://www.stjude.cloud) – a publically accessible pediatric genomic data resource requiring approval for controlled data access."
|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|
|GenomePaint||paper in progress|
|PeCan Pie||PeCan Pie paper|
|ChIP-Seq Peak Calling||unpublished|
|Rapid RNA-Seq Fusion Detection||paper in progress|
|Mutational Signatures||Mutational Patterns paper|
|cis-x||paper in progress|
|XenoCP||paper in progress|
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.
Any questions, comments, or concerns can be directed to our "Contact Us" form or you can email us directly at firstname.lastname@example.org.