Childhood Cancer Data Lab

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

When both methods agree on the cell type annotation for a sample, the module creates a unified consensus label. These consensus cell types are included in all processed and merged datasets from the Portal, in addition to the annotations from SingleR and CellAssign.

Visit scpca.alexslemonade.org!

OpenScPCA-analysis/analyses/cell-type-consensus at main · AlexsLemonade/OpenScPCA-analysis An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal - AlexsLemonade/OpenScPCA-analysis

We developed the cell-type-consensus module as part of the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project. It generates an ontology-aware consensus cell type label for every cell across all ScPCA samples, utilizing existing annotations obtained from SingleR and CellAssign.

Consensus cell types are now available on the #SingleCell #PediatricCancer Atlas (ScPCA) Portal! 🧵

🚨 Attention #SingleCell #PediatricCancer Atlas (ScPCA) Portal users! The Portal (scpca.alexslemonade.org) will be temporarily unavailable during scheduled updates starting May 7 at 7 PM EST.

Stay tuned! We’ve got exciting ScPCA news to share once we're back online.

Plus, visit our poster to discover the Open #SingleCell #PediatricCancer Atlas. We’re working with experts to analyze and enhance data from our ScPCA Portal. See our progress, get involved, and learn how contributors may become eligible for grants!

Find us today from 2-5 PM!
Section 4
Poster 18

The ALSF Data Lab and Grants teams are at #AACR25! Interested in learning how we can support your #PediatricCancer research? Connect with us at booth 3706.

Are you attending #AACR25? Visit us at booth 3706 from April 27-30 to apply in-person and learn more about our training workshops!

Data Lab Advanced Single-cell RNA-Seq Workshop, Philadelphia area, June 10-12, 2025 Applications are open for the Data Lab's next training workshop! We will cover advanced topics in the analysis of single-cell RNA-seq data for researchers studying pediatric cancer. The 3-day course w...

Applications are still open for our Advanced #SingleCell #RNASeq workshop!

Topics include:
-Integrating multiple single-cell RNA-seq libraries
-Differential expression analysis
-Working with CITE-Seq data
-Pathway analysis

Learn more and apply! ⬇️
www.ccdatalab.org/blog/data-la...

Alex’s Lemonade Stand Foundation at AACR 2025: Grants, workshops, and collaborative projects to accelerate your research! Are you attending the American Association for Cancer Research (AACR) Annual Meeting in Chicago, IL? Visit us in the exhibit hall at booth 3706 from April 27-30, 2025, and during poster sessions. We h...

We are heading to the #AACR Annual Meeting soon! You'll find us at booth 3706 from April 27-30. Stop by to learn about grants, collaborative projects, upcoming workshops and more.

We're also presenting the Open #SingleCell #PediatricCancer Atlas during a poster session.

More details below!

Interested in bringing our training program for #PediatricCancer researchers to your institution?

Learn more about our workshops at ccdatalab.org/data-science-workshops. Reach out to our team at training@ccdatalab.org!

Members of the Data Lab and Treehouse Childhood Cancer Initiative teams during a workshop.

This week, we brought our training program to the Treehouse #ChildhoodCancer Initiative at @ucscgenomics.bsky.social! We designed a workshop just for their team, covering #ReproducibleResearch practices, collaborative project management with Git/GitHub, analytical code review and more!

Introduction to Single-cell RNA-Seq Workshop (Virtual, August 4-8)

We will introduce:
-R programming and the Tidyverse R packages
-Single-cell RNA-seq data analysis
-Cell type annotation

Participants are not required to have prior experience with these topics. Read more & apply! ⬇️

Advanced Single-cell RNA-Seq Workshop (Philadelphia area, June 10-12)

Topics include:
-Integrating multiple single-cell RNA-seq libraries
-Differential expression analysis
-Pathway analysis

Some familiarity with basic R programming and single-cell RNA-Seq is required. Read more & apply! ⬇️

We’re excited to announce two opportunities for #PediatricCancer researchers to build their skills in #SingleCell #RNASeq data analysis this summer! Applications are open for our introductory and advanced workshops. 🧵

This week, we’re holding our first workshop of the year and we plan to announce more 2025 training opportunities soon. Join our mailing list to be notified when applications open! bit.ly/3eQZXGQ

YouTube video by Pediatric Oncology Knowledge Center Accelerating Childhood Cancer Research through Data Science Training Workshops

Hear from Drs. Eric Wafula and Elena Vasileva who sat down with us to share their experiences at Data Lab training workshops! Learn why they believe our #SingleCell #RNASeq courses are essential for #PediatricCancer researchers who want to perform their own analysis.