The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors
6 affiliations
- 1Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- 2Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA; The University of Texas MD Anderson Cancer Center, UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- 3Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA; Translational Research, Multiple Myeloma Research Foundation, Norwalk, CT 06851, USA
- 4Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- 5Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA; Center for Health AI, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- 6Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA. Electronic address: [email protected]
Abstract
The Single-Cell Pediatric Cancer Atlas (ScPCA) Portal is a resource for uniformly processed single-cell and single-nucleus RNA sequencing (RNA-seq) data and de-identified metadata from pediatric tumor samples. Originally comprising data from 10 projects funded by Alex's Lemonade Stand Foundation (ALSF), the Portal currently contains summarized gene expression data for over 700 samples across 55 cancer types from ALSF-funded and community-contributed datasets. Downloads include expression data as SingleCellExperiment or AnnData objects containing raw and normalized counts, principal-component analysis (PCA) and uniform manifold approximation and projection (UMAP) coordinates, automated cell-type annotations, and copy-number variation estimates, along with summary reports. Some samples have additional data from bulk RNA-seq, spatial transcriptomics, and/or feature barcoding (e.g., CITE-seq) included in the download. All data on the Portal were uniformly processed using scpca-nf, an efficient and open-source Nextflow workflow that uses alevin-fry to quantify gene expression. Comprehensive documentation, including file descriptions and a getting-started guide, are available online.
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BibTeX
@article{hawkins2026singlecell,
title = {{The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors}},
author = {Allegra G. Hawkins and Joshua A. Shapiro and Stephanie J. Spielman and David S. Mejia and Deepashree Venkatesh Prasad and Nozomi Ichihara and Arkadii Yakovets and Avrohom M. Gottlieb and Kurt G. Wheeler and Chanté J. Bethell and Steven M. Foltz and Jennifer O’Malley and Casey S. Greene and Jaclyn Taroni},
journal = {Cell Genomics},
year = {2026},
month = jun,
doi = {10.1016/j.xgen.2026.101283},
url = {https://doi.org/10.1016/j.xgen.2026.101283},
note = {CC BY},
}
RIS
TY - JOUR
TI - The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors
AU - Allegra G. Hawkins
AU - Joshua A. Shapiro
AU - Stephanie J. Spielman
AU - David S. Mejia
AU - Deepashree Venkatesh Prasad
AU - Nozomi Ichihara
AU - Arkadii Yakovets
AU - Avrohom M. Gottlieb
AU - Kurt G. Wheeler
AU - Chanté J. Bethell
AU - Steven M. Foltz
AU - Jennifer O’Malley
AU - Casey S. Greene
AU - Jaclyn Taroni
PY - 2026
DA - 2026/06/24
JO - Cell Genomics
DO - 10.1016/j.xgen.2026.101283
UR - https://doi.org/10.1016/j.xgen.2026.101283
AB - The Single-Cell Pediatric Cancer Atlas (ScPCA) Portal is a resource for uniformly processed single-cell and single-nucleus RNA sequencing (RNA-seq) data and de-identified metadata from pediatric tumor samples. Originally comprising data from 10 projects funded by Alex's Lemonade Stand Foundation (ALSF), the Portal currently contains summarized gene expression data for over 700 samples across 55 cancer types from ALSF-funded and community-contributed datasets. Downloads include expression data as SingleCellExperiment or AnnData objects containing raw and normalized counts, principal-component analysis (PCA) and uniform manifold approximation and projection (UMAP) coordinates, automated cell-type annotations, and copy-number variation estimates, along with summary reports. Some samples have additional data from bulk RNA-seq, spatial transcriptomics, and/or feature barcoding (e.g., CITE-seq) included in the download. All data on the Portal were uniformly processed using scpca-nf, an efficient and open-source Nextflow workflow that uses alevin-fry to quantify gene expression. Comprehensive documentation, including file descriptions and a getting-started guide, are available online.
SN - 2666-979X
ER -