The Childhood Cancer Data Lab, founded by @alexslemonade, is at the intersection of big data and childhood cancer research. Read our blog: https://xitter.cf/t.co/7GRvCQQrOn
Philadelphia area & worldwide
Joined June 2017
- Tweets735
- Following237
- Followers868
- Likes243
Our Director, Jaclyn Taroni, is giving two talks on the Single-cell Pediatric Cancer Atlas (ScPCA) this month, each for a different audience. 🧵
She'll also preview the Portal's upcoming integration with the CCDI ecosystem and discuss OpenScPCA, our open science project for transparently trying new approaches with ScPCA data, plus the architecture that supports long-lived collaborative projects.
Oct 14, 2:30 PM ET, Ladders 2 Cures Accelerator Meeting: Each pediatric cancer is a rare disease, so data aggregated across institutions is a force multiplier. This talk covers building ScPCA for reuse, with lessons for rare disease data resources. Join: broad.io/L2CAM
Our paper on the Single-cell Pediatric Cancer Atlas (ScPCA) Portal is out now in @CellGenomics 🎉
ScPCA is a free resource of uniformly processed single-cell & single-nuclei RNA-seq data from pediatric tumors and model systems.
📄 doi.org/10.1016/j.xgen.2026.…
What's on the Portal:
🔬 700 samples across 55 pediatric cancer types
🧬 Single-cell, single-nuclei, bulk RNA-seq, spatial & CITE-seq
📦 Download-ready SingleCellExperiment & AnnData objects (raw + normalized counts, PCA/UMAP, automated cell type annotations)
📢 Have single-cell or spatial txomics data from pediatric tumors or model systems? We'd love to help you share it on the Portal.
Contribute your dataset, make it openly available, and you may be eligible for a small grant for childhood cancer research.
scpca.alexslemonade.org/cont…
We had a great time being part of #AACR26 — sharing resources like our Single-cell Pediatric Cancer Atlas Portal, meeting @AlexsLemonade grant recipients, and learning about the latest advancements in cancer research.
Learn more about the Data Lab: ccdatalab.org
Childhood Cancer Data Lab retweeted
Dr. Kelly Bailey from the Mayo Clinic with Ally Hawkins, PhD from the ALSF Data Lab at AACR 2026!
We’re proud to collaborate with Dr. Bailey’s team on the Sean Karl cohort, working to better understand therapeutic vulnerabilities in Ewing sarcoma.
Our team has contributed by developing a reproducible workflow to generate a harmonized dataset for consistent analyses, which will be released and openly licensed for others’ use. The generated data will be shared on the Single-cell Pediatric Cancer Atlas (ScPCA) Portal.
Come meet Dr. Hawkins at our poster today to learn more about the ScPCA Portal!
Poster: Improving the utility of the Single-cell Pediatric Cancer Atlas through updated cell type annotations, CNV inference, and visualization tools
📅 Today! April 20 | 2-5 PM
📍 Section 31 | Board 13
Meet the Data Lab at #AACR26! 🎉
Stop by Booth 2918 to meet our team and explore resources to accelerate new treatment and cure discovery for pediatric cancer.
We're gearing up for the 2026 #AACR Annual Meeting in San Diego, CA! 🎉
Find us in the exhibit hall at booth 2918! Learn about ALSF grant opportunities, resources for #PediatricCancer research, and apply to free data science training workshops.
ccdatalab.org/blog/alsf-at-a…
We're excited to join the Childhood Cancer Data Initiative (CCDI) webinar series! 🎉
Our director, Dr. Jaclyn N. Taroni, will give a lightning talk on the Open #SingleCell #PediatricCancer Atlas project.
🗓 Tomorrow! April 7 | 10:30 AM–12 PM
events.cancer.gov/ccdi/webin…
Are you attending #ENAR2026 in Indianapolis next week? Don’t miss the Data Lab’s presentation on machine learning in pediatric cancer research, presented by our director Dr. Jaclyn N. Taroni, on March 16!
#MachineLearning #PediatricCancer
Applications are open! We’re excited to announce two opportunities for pediatric cancer researchers to build their skills in single-cell RNA-Seq data analysis.
Learn more and apply to our upcoming workshops. 🧵
Introduction to Single-cell RNA-Seq Workshop (Virtual, May 11-15)
We will introduce:
-R programming, R Notebooks, and reproducible research practices
-Select pipelines for single-cell RNA-seq analysis
-Cell type annotation
ccdatalab.org/blog/virtual-i…
Advanced Single-cell RNA-Seq Workshop (Virtual, June 8-12)
We will cover:
-Integrating multiple single-cell RNA-seq libraries
-Working with CITE-Seq data
-Differential expression analysis
-Pathway analysis
ccdatalab.org/blog/virtual-a…
Advanced Single-cell RNA-Seq Workshop (Virtual, June 8-12)
We will cover:
-Integrating multiple single-cell RNA-seq libraries
-Working with CITE-Seq data
-Differential expression analysis
-Pathway analysis
ccdatalab.org/blog/virtual-a…
Did you know the Data Lab can support your data-intensive research projects? Our science team specializes in working with large datasets from designing pipelines to ensuring reproducible analysis.
Learn more! ccdatalab.org/scientific-col…
📢Exciting news from the #SingleCell #PediatricCancer Atlas Portal! We’ve rolled out new features to help you extract deeper insights from your ScPCA datasets.
Read our blog to see how these updates can help you save time and work more efficiently.
ccdatalab.org/blog/new-featu…
Doublet detection:
We ran doublet detection on all samples using scDblFinder. We do not remove doublets, but these results are now included in the filtered and processed objects for downstream filtering.
InferCNV:
We now perform copy number variation inference using InferCNV on samples that contain at least 100 non-malignant reference cells, based on updated consensus cell types. The InferCNV output is available in processed objects and can aid in identifying malignant cells.
Stay tuned! We’ll be announcing even more new features early next year. Until then, explore these updates at scpca.alexslemonade.org. 🚀
