ScPCA Portal Documentation

This is the documentation for the Single-cell Pediatric Cancer Atlas Portal. The ScPCA Portal is a database of single-cell and single-nuclei RNA-sequencing data from pediatric cancer clinical samples and xenografts.

• Processing information
  • Single-cell and single-nuclei RNA-seq
    • Mapping and quantification using alevin-fry
      • Reference transcriptome index
      • Selective alignment
      • Alevin-fry parameters
    • Post alevin-fry processing
      • Combining counts from spliced cDNA and intronic regions
      • Filtering cells
    • Processed gene expression data
  • ADT quantification from CITE-seq experiments
    • Combining ADT counts with RNA counts
    • Processed ADT data
  • Multiplexed libraries
    • Hashtag oligonucleotide (HTO) quantification
    • HTO demultiplexing
    • Genetic demultiplexing
  • Spatial transcriptomics
    • Mapping and quantification using Space Ranger
  • Bulk RNA samples
    • Preprocessing with fastp
    • Mapping and quantification using salmon
      • Salmon parameters
• Downloadable files
  • Download folder structure for project downloads:
  • Download folder structure for individual sample downloads:
  • Gene expression data
  • QC Report
  • Metadata
  • Multiplexed sample libraries
  • Spatial transcriptomics libraries
• Single-cell gene expression file contents
  • Components of a SingleCellExperiment object
    • Expression counts
    • Cell metrics
    • Gene information and metrics
    • Experiment metadata
    • Dimensionality reduction results
  • Additional SingleCellExperiment components for CITE-seq libraries (with ADT tags)
  • Additional SingleCellExperiment components for multiplexed libraries
    • Demultiplexing results
    • Additional demultiplexing statistics
• Getting started with an ScPCA dataset
  • Importing ScPCA data into R
  • Working with the processed SingleCellExperiment objects
  • Working with the filtered SingleCellExperiment objects
    • Quality control
    • Normalization
    • Dimensionality Reduction
  • What if I want to use Seurat?
  • What if I want to use scanpy?
  • Special considerations for CITE-seq experiments
    • Filtering cells based on ADT quality control
  • Special considerations for multiplexed samples
• Frequently Asked Questions
  • Why did we use Alevin-fry for processing?
  • How do I use the provided RDS files in R?
  • What is the difference between samples and libraries?
  • Why do some samples have missing participant IDs?
  • What is a multiplexed sample?
  • Why are demultiplexed samples not available?
  • What are estimated demux cell counts?
  • What genes are included in the reference transcriptome?
  • Where can I see the code for generating QC reports?
  • What if I want to use Seurat instead of Bioconductor?
  • What if I want to use Python instead of R?
  • Why doesn’t my existing code work on a new download from the Portal?
• How to Cite
  • Citing a project
  • Citing the ScPCA Portal
    • APA Format
    • MLA Format
• CHANGELOG
  • 2023.11.10