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Childhood Cancer Data Lab @cancerdatalab.bsky.social · 8d

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

An example of downloading a project from the ScPCA Portal.

Childhood Cancer Data Lab @cancerdatalab.bsky.social · 8d

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

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · 8d

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

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

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · 8d

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

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · 13d

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

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · 15d

🗓️ 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!

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · 15d

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! 🧵

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · 19d

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!

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...

www.ccdatalab.org

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Sep 8

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

Childhood Cancer Data Lab @cancerdatalab.bsky.social · Sep 8

📍 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!

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Sep 8

📍 #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).

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Sep 8

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! 🧵

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Aug 20

📣 Upcoming workshop!

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

Learn more and apply. ⤵️

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...

www.ccdatalab.org

Childhood Cancer Data Lab @cancerdatalab.bsky.social · Aug 20

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!

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Aug 4

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!

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...

www.ccdatalab.org

Childhood Cancer Data Lab @cancerdatalab.bsky.social · Aug 4

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. 🧵

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Jul 24

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

Childhood Cancer Data Lab @cancerdatalab.bsky.social · Jul 24

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

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Jul 16

📣 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.

Childhood Cancer Data Lab @cancerdatalab.bsky.social · Jul 1

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

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...

www.biorxiv.org

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Jul 1

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

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Jul 1

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!

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

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Jul 1

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! 🧵

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Jun 12

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

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Childhood Cancer Data Lab @cancerdatalab.bsky.social · Jun 12

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.

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