The scpdata package distributes mass spectrometry-based single-cell proteomics datasets. The datasets were collected from published work and formatted to a standardized data framework. The scp frameworks stores the expression data for different MS levels (identified spectrum, peptide, or protein) in separate assays. Each assay is an object of class SingleCellExperiment that allows easy integration with state-of-the-art single-cell analysis tools. All assays are contained in a single object of class QFeatures. An overview of the data structure is shown provided in the scp package.

The scpdata() function returns a summary table with all currently available datasets in the package. More information about the data content and the data collection can be found in the corresponding manual pages.

scpdata()

Value

A DataFrame table containing a summary of the available datasets.

See also

More information about the data manipulation can be found in the scp package.

Author

Christophe Vanderaa

Examples

## List available datasets and their metadata 
scpdata()
#> DataFrame with 30 rows and 15 columns
#>                title  dataprovider       species taxonomyid      genome
#>          <character>   <character>   <character>  <integer> <character>
#> EH3899 specht2019... SlavovLab ... Homo sapie...       9606          NA
#> EH3900 specht2019... SlavovLab ... Homo sapie...       9606          NA
#> EH3901 dou2019_ly...       MassIVE Homo sapie...       9606          NA
#> EH3902 dou2019_mo...       MassIVE Mus muscul...      10090          NA
#> EH3903 dou2019_bo...       MassIVE Mus muscul...      10090          NA
#> ...              ...           ...           ...        ...         ...
#> EH9498 petrosius2...     Dataverse Homo sapie...       9606          NA
#> EH9609     krull2024         PRIDE Homo sapie...       9606          NA
#> EH9610 hu2023_K56...       MassIVE Homo sapie...       9606          NA
#> EH9611 hu2023_ooc...       MassIVE Homo sapie...       9606          NA
#> EH9627       ai2025a       MassIVE Homo sapie...       9606          NA
#>          description coordinate_1_based    maintainer rdatadateadded
#>          <character>          <integer>   <character>    <character>
#> EH3899 SCP expres...                  1 Christophe...     2020-11-05
#> EH3900 SCP expres...                  1 Christophe...     2020-11-05
#> EH3901 SCP expres...                  1 Christophe...     2020-11-05
#> EH3902 SCP expres...                  1 Christophe...     2020-11-05
#> EH3903 SCP expres...                  1 Christophe...     2020-11-05
#> ...              ...                ...           ...            ...
#> EH9498 Single-cel...                  1 Samuel Gre...     2024-04-11
#> EH9609 Single-cel...                  1 Enes Sefa ...     2024-11-13
#> EH9610 Single-cel...                  1 Enes Sefa ...     2024-11-13
#> EH9611 Single-cel...                  1 Enes Sefa ...     2024-11-13
#> EH9627 Single-cel...                  1 Laurent Ga...     2025-03-06
#>        preparerclass                                          tags
#>          <character>                                        <AsIs>
#> EH3899       scpdata Experiment...,Expression...,Experiment...,...
#> EH3900       scpdata Experiment...,Expression...,Experiment...,...
#> EH3901       scpdata Experiment...,Expression...,Experiment...,...
#> EH3902       scpdata Experiment...,Expression...,Experiment...,...
#> EH3903       scpdata Experiment...,Expression...,Experiment...,...
#> ...              ...                                           ...
#> EH9498       scpdata      Expression...,MassSpectr...,Proteome,...
#> EH9609       scpdata      Expression...,MassSpectr...,Proteome,...
#> EH9610       scpdata      Expression...,MassSpectr...,Proteome,...
#> EH9611       scpdata      Expression...,MassSpectr...,Proteome,...
#> EH9627       scpdata      Expression...,MassSpectr...,Proteome,...
#>           rdataclass     rdatapath     sourceurl  sourcetype
#>          <character>   <character>   <character> <character>
#> EH3899     QFeatures scpdata/sp... https://sc...         CSV
#> EH3900     QFeatures scpdata/sp... https://sc...         CSV
#> EH3901     QFeatures scpdata/do... ftp://mass...    XLS/XLSX
#> EH3902     QFeatures scpdata/do... ftp://mass...    XLS/XLSX
#> EH3903     QFeatures scpdata/do... ftp://mass...    XLS/XLSX
#> ...              ...           ...           ...         ...
#> EH9498     QFeatures scpdata/pe... https://da...         TXT
#> EH9609     QFeatures scpdata/kr... https://ww...         TXT
#> EH9610 SingleCell... scpdata/hu... ftp://mass...         TXT
#> EH9611 SingleCell... scpdata/hu... ftp://mass...         TXT
#> EH9627     QFeatures scpdata/ai... ftp://mass...         TXT

## Load data using the ExperimentHub interface
hub <- ExperimentHub()

if (FALSE) { # \dontrun{
## Download the data set of interest using ExperimentHub indexing
hub[["EH7711"]]
## Download the same data set using the build-in function
leduc2022()
} # }