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-identified metadata from pediatric tumor samples. Originally comprised of data from 10 projects funded by Alex’s Lemonade Stand Foundation, the Portal currently contains summarized gene expression data for over 500 samples from over 50 types of cancers from ALSF-funded and community-contributed datasets. In addition to gene expression data from single-cell and single-nuclei RNA-seq, the Portal holds data obtained from bulk RNA-seq, spatial transcriptomics, and feature barcoding methods, such as CITE-seq and cell hashing. ScPCA data are available for download as SingleCellExperiment or AnnData objects and are ready for downstream analyses. Objects include raw counts and normalized gene expression data, PCA and UMAP coordinates, and automated cell type annotations. Additionally, all downloads