Childhood Cancer Data Lab

Data Lab Advanced Single-Cell RNA-Seq Workshop, Virtual, December 8-12, 2025 Applications are open for the Data Lab's upcoming workshop, which will cover advanced topics in the analysis of single-cell RNA-seq data for researchers studying pediatric cancer. The course will be h...

What you will learn:
-Integration of multiple single-cell RNA-seq libraries
-Approaches to differential expression analyses with single-cell data
-Working with CITE-seq data
-Common approaches for pathway analysis

Learn more and apply below!

📣 Applications are open for our final workshop of the year!

If you're a #PediatricCancer researcher looking to build on your foundational skills in #SingleCell #RNASeq analysis, this workshop may be for you.

🎓 Topic: Advanced Single-cell RNA-Seq
📅 Date/Time: December 8-12, 2025
📍 Virtual

An example of downloading a project from the ScPCA Portal.

📊 Access rich datasets that include data, metadata, and expertly curated cell type annotations…for free!

A project page on the ScPCA Portal.

🔍 User-friendly search and filter tools allow you to quickly find the projects you’re interested in.

Homepage of the Single-cell Pediatric Cancer Atlas (ScPCA) Portal.

🔬Explore over 700 samples from 55 pediatric cancer types, all in one place.

Attending the NCI Office of Data Sharing Annual Symposium? Stop by our table during poster/demo sessions for a live look at the Single-cell Pediatric Cancer Atlas Portal (scpca.alexslemonade.org).

📆 September 30 (today!) & October 1
📍 Poster/demo sessions

#SingleCell #PediatricCancer #DataSharing

Connect with our team at the #AACR Special Conference: Discovery and Innovation in #PediatricCancer! Dr. Ally Hawkins will be presenting our work on a collaboration aimed at uncovering therapeutic vulnerabilities in #EwingSarcoma.

🗓️ Tonight (9/25) | 7-9:30PM
📍 Poster Session A

🗓️ September 25 | 7-9:30 PM
📍 Poster Session A
🧾 "ews-nf: A custom workflow for tumor cell annotation and analysis of single-cell RNA-sequencing of paired patient Ewing sarcoma specimens from the Sean Karl cohort"

Connect with us at AACR and explore how we can support your research too!

Are you attending the #AACR Special Conference: Discovery and Innovation in #PediatricCancer? Stop by our poster to learn how we're collaborating with other labs to tackle their complex data challenges! 🧵

Pediatric Cancer Researchers Driving Progress Through Data, Training, and Collaboration At the Childhood Cancer Data Lab, we support pediatric cancer researchers by providing data science training, collaborating on data-intensive projects, and designing open-source tools. Through this wo...

September is #ChildhoodCancerAwarenessMonth, a time to recognize the urgent need for better treatments and outcomes for kids with cancer. In our latest blog, we’re highlighting a few researchers who have drawn on the Data Lab’s resources in their remarkable efforts to accelerate new cure discovery!

Are you presenting at any of these events? Drop your poster or demo info in the comments. We hope to see you there!

📍 NCI Office of Data Sharing Annual Symposium

Learn how to access and use pediatric cancer data that may align with your research interests! Catch our live demo of the #SingleCell #PediatricCancer Atlas (ScPCA) Portal.

📆 Stop by our table during poster/demo sessions on September 30 and October 1!

📍 #AACR Special Conference in Cancer Research - Discovery and Innovation in #PediatricCancer

We’re showcasing an ongoing collaboration, supporting a multi-institutional effort to understand the therapeutic vulnerabilities of #EwingSarcoma.

📆 Poster Session A on September 25 (7-9:30 PM).

This fall, the Data Lab is hitting the road to present some of our tools and projects during these exciting events. Here’s where you can find us! 🧵

Level Up Your Reproducible Research Skills at Our Next Workshop! At the Childhood Cancer Data Lab, we’re committed to helping pediatric cancer researchers work more efficiently, collaboratively, and reproducibly. That’s why we created our Reproducible Research Prac...

📣 Upcoming workshop!

Topic: Reproducible Research Practices
Dates: November 6-7, 2025
Location: Philadelphia, PA

Learn more and apply. ⤵️

What can #PediatricCancer researchers expect from a Data Lab workshop?

✅ Interactive, hands-on training
✅ Instructors who take the time to understand your research goals
✅ Ongoing support with opportunities for 1:1 consultation, even after the workshop ends!

Level Up Your Reproducible Research Skills at Our Next Workshop! At the Childhood Cancer Data Lab, we’re committed to helping pediatric cancer researchers work more efficiently, collaboratively, and reproducibly. That’s why we created our Reproducible Research Prac...

Whether you're looking to set up efficient processes in your lab, improve your ability to share data and code, or manage a collaborative project, this workshop can set you up for success.

🚀 Read our blog for full details and to apply!

Our #ReproducibleResearch Practices workshop teaches tools and techniques to help #PediatricCancer researchers work more efficiently, collaboratively, and reproducibly. The next course is taking place November 6–7, 2025, in Philadelphia, PA. 🧵

🚀 Easily download 700 samples from over 55 pediatric cancer types at scpca.alexslemonade.org!

Here’s what you’ll get with each dataset you download from the #SingleCell #PediatricCancer Atlas (ScPCA) Portal…for free!

-Unfiltered, filtered & processed counts
-QC report
-Associated metadata
-Reliable cell type annotations

📣 Join the Open #SingleCell #PediatricCancer Atlas (OpenScPCA) project. Grants are available!

We aim to annotate cell types for 19 projects on the ScPCA Portal. Explore the grant table to see which cancer types need your insight: github.com/AlexsLemonade/OpenScPCA-analysis/discussions/1062.

The Single-cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors The Single-cell Pediatric Cancer Atlas (ScPCA) Portal (<https://scpca.alexslemonade.org/>) is a data resource for uniformly processed single-cell and single-nuclei RNA sequencing (RNA-seq) data and de...

Check out the ScPCA preprint on bioRxiv for more details about these updates, and visit scpca.alexslemonade.org to download the data!

Figure 6 from the ScPCA preprint: Comparison of bulk and pseudo-bulk modalities.

Several projects on the Portal contain bulk RNA-seq data in addition to single-cell/nuclei RNA-seq data. We compared modalities across five solid tumor projects to explore potential biological differences.

Figure 5 from the ScPCA preprint: Consensus cell type annotations in Brain and CNS tumors.

Using an ontology-based approach, we have assigned consensus cell types to all samples on the ScPCA Portal. They are now included in all processed and merged datasets from the Portal!

We’ve made exciting updates to the #SingleCell #PediatricCancer Atlas (ScPCA) Portal, making the available data even more robust, reliable, and useful for the research community! 🧵

Upcoming training opportunities!
-Reproducible Research Practices: November 2025
-Advanced Single-cell RNA-Sequencing: December 2025

Are you are a #PediatricCancer researcher interested in attending one of these workshops? Sign up to be notified when applications open!

✉️: bit.ly/3eQZXGQ

Thank you to everyone who joined us to learn advanced topics in #SingleCell #RNAseq analysis this week. We look forward to hosting more researchers at our workshops this year.

Building Reproducible Research Skills: A Training Workshop with the Treehouse Childhood Cancer Initiative The Data Lab recently traveled to California to lead a hands-on workshop for nine researchers from the UC Santa Cruz Treehouse Childhood Cancer Initiative. The participants, all from a range of backgr...

We teamed up with the Treehouse Childhood Cancer Initiative at @ucscgenomics.bsky.social to deliver a custom workshop on reproducible research. In our new blog, Dr. Holly Beale, Lead Computational Biologist at Treehouse, shares how their team is putting new skills into practice. Read the full story!

Use cases as a brainstorming tool ‍Use cases define how users interact with a product or system, including actions users can take and how the system responds. It also identifies user goals and paths for the system to handle errors.

Design and engineering teams utilize use cases to build a shared understanding of what a product does and how users might interact with it.

In our latest blog post, our #UX Designer details the unique way we apply use cases to guide smarter design decisions—right from the start of a project!

Training Topics Survey In 2018, the ALSF Childhood Cancer Data Lab launched a training program to teach pediatric cancer researchers the data science skills they need to better analyze their own data. We have trained nearly...

The Data Lab is exploring new topics to expand our training program! We invite #PediatricCancer researchers who work with high-dimensional data to take a 10-min survey that will help shape future learning opportunities for the community.

🚀 Take our survey! forms.gle/J9YztY4r5BQ1ch66A