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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
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
Downloadable files
SingleCellExperiment
downloads
Download folder structure for project downloads:
Download folder structure for individual sample downloads:
AnnData
downloads
Download folder structure for project downloads:
Download folder structure for individual sample downloads:
Download folder structure for individual sample downloads with CITE-seq (ADT) data:
Gene expression data
QC report
Cell type report
Metadata
Multiplexed sample libraries
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:
Spatial transcriptomics libraries
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
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 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?
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
Citing a project
Citing the ScPCA Portal
CHANGELOG
2024.04.26
2024.04.18
2024.04.11
2024.03.08
2023.11.10
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