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  • 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
        • Cell type annotation
        • CNV inference
    • 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
    • Merged objects
  • Download options
    • Data format
    • Modalities
    • Merged objects
    • Multiplexed sample libraries
  • Downloadable files
    • Project downloads
      • Download folder structure for SingleCellExperiment project downloads:
      • Download folder structure for AnnData project downloads:
      • Download folder structure for AnnData project downloads with CITE-seq (ADT) data:
      • Merged object downloads
        • Download folder structure for SingleCellExperiment merged downloads:
        • Download folder structure for AnnData merged downloads:
        • Download folder structure for AnnData merged downloads with CITE-seq (ADT) data:
    • Custom datasets
      • Download folder structure for custom downloads:
    • Portal-wide Downloads
      • SingleCellExperiment Portal-wide download structure
      • AnnData Portal-wide download structure
      • Spatial Portal-wide download structure
      • Portal-wide downloads as merged objects
        • Portal-wide download structure for merged SingleCellExperiment objects
        • Portal-wide download structure for merged AnnData objects
      • Metadata-only downloads
    • Gene expression data
    • QC report
    • Cell type report
    • Metadata
    • Multiplexed sample libraries
    • Spatial transcriptomics libraries
    • Bulk RNA-seq
    • Programmatic downloads from the ScPCA Portal
  • 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
      • AnnData expression counts
      • AnnData cell metrics
      • AnnData gene information and metrics
      • AnnData experiment metadata
      • AnnData dimensionality reduction results
      • Additional AnnData components for CITE-seq libraries (with ADT tags)
  • 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
      • AnnData expression counts
      • AnnData cell metrics
      • AnnData gene information and metrics
      • AnnData experiment metadata
      • AnnData dimensionality reduction results
      • Additional AnnData components for CITE-seq libraries (with ADT tags)
  • Getting started with an ScPCA dataset
    • Importing ScPCA data from SingleCellExperiment objects into R
    • Importing ScPCA data from AnnData objects into Python
    • Working with processed objects
      • Gene expression data
      • Quality control data
      • Dimensionality reduction
      • Highly variable genes
      • Clustering
      • Cell type annotation
        • Submitter-provided annotations
        • SingleR annotations
        • CellAssign annotations
        • Additional cell type resources
    • Working with a merged ScPCA object
      • Analyses with merged objects
      • Subsetting the merged object
    • What if I want to use Seurat?
    • Special considerations for CITE-seq experiments
      • Filtering cells based on ADT quality control
      • Using MuData objects for multimodal analysis
    • 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?
    • How do I use the provided H5AD files in Python?
    • Which samples can I download as AnnData objects?
    • What if I want to use MuData instead of 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?
    • Which libraries include CNV inferences?
    • Where can I find the inferCNV heatmap?
    • 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 can’t I merge a subset of samples from a project?
    • 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 can I use the command line tools link to download data?
    • Can I download data from the Portal programmatically?
    • Why can’t I change the data format in My Dataset?
    • Why did project options change when I appended samples to My Dataset?
    • Why are some values different after I regenerate My Dataset?
  • How to Cite
    • Citing a project
    • Citing the ScPCA Portal
  • CHANGELOG
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