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ScPCA Portal Docs
2023.11.02
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?
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