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
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
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 single-cell workshops. 🧵
Quote from Dr. Anthony Cillo about collaborating with the Data Lab: "It’s amazing to generate large genomics datasets from patient samples, but extracting biologically relevant information from such complex data can be challenging. By working with the Data Lab, we’ve been able to address many of these obstacles. This was made possible by their team’s ability and willingness to work closely with us and to lead the development of a state-of-the-art, reproducible workflow. The result is a harmonized dataset that will be tremendously helpful for our own research and for the field of Ewing sarcoma.”
Collaborate with us! 🧑🔬👩💻
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-collaboration
Exciting news from the #SingleCell #PediatricCancer Atlas (ScPCA) Portal! We’ve rolled out a suite of 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.
Stay tuned! We’ll be announcing even more new features early next year. Until then, explore these updates at scpca.alexslemonade.org. 🚀
InferCNV:
We now perform copy number variation (CNV) 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.
This year, we’ve added OpenScPCA annotations to downloads for two ScPCA projects:
-SCPCP000004 #Neuroblastoma
-SCPCP000015 #EwingSarcoma
Learn more about OpenScPCA! openscpca.readthedocs.io/en/latest/
OpenScPCA cell type annotations:
Automated, reference-based methods have considerable limitations when applied to pediatric malignant cells. We launched the OpenScPCA project in 2024 to collaboratively improve cell type annotation.
Improved cell type annotations:
Every sample now includes automated cell type labels from SCimilarity, SingleR, and CellAssign. When two of three methods agree, an ontology-based consensus label is assigned. We expect this to be most useful for helping users quickly identify non-malignant cells!
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.
🎉 As we wrap up the year, we’re excited to share new updates to the #SingleCell #PediatricCancer Atlas (ScPCA) Portal! All datasets have been updated with features that improve data quality and usability.
Here’s what’s new! 🧵
📣 New blog post!
Starting a new scientific research project? Make life easier for your future self! Check out this guide from Data Lab on organizing your code, files, and workflows so your research stays reproducible.
#ReproducibleResearch #OpenScience
Applications are still open! Expand your data analysis skills during our Advanced Single-Cell RNA-seq Workshop for pediatric cancer researchers.
📆 December 8-12, 2025
💻 Virtual
⬇️ Learn more and apply!
#PediatricCancer #SingleCell #RNASeq
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! 🧵
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! 🧵
📣 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!
