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 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.