scpdata.RdThe 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::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::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()A DataFrame table containing a summary of the available
datasets.
More information about the data manipulation can be found
in the scp package.
## 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()
} # }