ScPCA Portal Documentation
This is the documentation for the Single-cell Pediatric Cancer Atlas Portal. The ScPCA Portal is a growing database of uniformly processed single-cell data from pediatric cancer tumors and model systems.
- Processing information
- Downloadable files
- Single-cell gene expression file contents
- Components of a SingleCellExperiment object
- SingleCellExperiment expression counts
- SingleCellExperiment cell metrics
- SingleCellExperiment gene information and metrics
- SingleCellExperiment experiment metadata
- SingleCellExperiment sample metadata
- SingleCellExperiment dimensionality reduction results
- Additional SingleCellExperiment components for CITE-seq libraries (with ADT tags)
- Additional SingleCellExperiment components for multiplexed libraries
- Demultiplexing results
- Additional demultiplexing statistics
- Components of an AnnData object
- Components of a SingleCellExperiment object
- Merged objects
- Components of a SingleCellExperiment merged object
- SingleCellExperiment expression counts
- SingleCellExperiment cell metrics
- SingleCellExperiment gene information and metrics
- SingleCellExperiment experiment metadata
- SingleCellExperiment sample metadata
- SingleCellExperiment dimensionality reduction results
- Additional SingleCellExperiment components for CITE-seq libraries (with ADT tags)
- Additional SingleCellExperiment components for multiplexed libraries
- Components of an AnnData merged object
- Components of a SingleCellExperiment merged object
- Getting started with an ScPCA dataset
- Importing ScPCA data from
SingleCellExperimentobjects into R - Importing ScPCA data from
AnnDataobjects into Python - Working with processed objects
- Working with a merged ScPCA object
- What if I want to use Seurat?
- Special considerations for CITE-seq experiments
- Special considerations for multiplexed samples
- Importing ScPCA data from
- Frequently Asked Questions
- Why did we use Alevin-fry for processing?
- How do I use the provided RDS files in R?
- How do I use the provided H5AD files in Python?
- Which samples can I download as AnnData objects?
- What is the difference between samples and libraries?
- What is a participant ID?
- 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?
- Which libraries include cell type annotations?
- What if I want to use Seurat instead of Bioconductor?
- When should I download a project as a merged object?
- Which projects can I download as merged objects?
- Why doesn’t my existing code work on a new download from the Portal?
- I previously downloaded a sample that is no longer on the Portal. Why can’t I find it?
- How to Cite
- CHANGELOG