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
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()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 26 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
#> ... ... ... ... ... ...
#> EH9450 gregoire20... PRIDE Homo sapie... 9606 NA
#> EH9477 khan2023 MassIVE Homo sapie... 9606 NA
#> EH9487 guise2024 MassIVE Homo sapie... 9606 NA
#> EH9497 petrosius2... Dataverse Homo sapie... 9606 NA
#> EH9498 petrosius2... Dataverse 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
#> ... ... ... ... ...
#> EH9450 Single-cel... 1 Samuel Gre... 2024-02-12
#> EH9477 Single-cel... 1 Enes Sefa ... 2024-03-08
#> EH9487 Single-cel... 1 Christophe... 2024-04-08
#> EH9497 Mouse embr... 1 Enes Sefa ... 2024-04-11
#> EH9498 Single-cel... 1 Samuel Gre... 2024-04-11
#> preparerclass tags rdataclass
#> <character> <AsIs> <character>
#> EH3899 scpdata Experiment...,Expression...,Experiment...,... QFeatures
#> EH3900 scpdata Experiment...,Expression...,Experiment...,... QFeatures
#> EH3901 scpdata Experiment...,Expression...,Experiment...,... QFeatures
#> EH3902 scpdata Experiment...,Expression...,Experiment...,... QFeatures
#> EH3903 scpdata Experiment...,Expression...,Experiment...,... QFeatures
#> ... ... ... ...
#> EH9450 scpdata Expression...,MassSpectr...,Proteome,... QFeatures
#> EH9477 scpdata Expression...,MassSpectr...,Proteome,... QFeatures
#> EH9487 scpdata Expression...,MassSpectr...,Proteome,... QFeatures
#> EH9497 scpdata Expression...,MassSpectr...,Proteome,... QFeatures
#> EH9498 scpdata Expression...,MassSpectr...,Proteome,... QFeatures
#> rdatapath sourceurl sourcetype
#> <character> <character> <character>
#> EH3899 scpdata/sp... https://sc... CSV
#> EH3900 scpdata/sp... https://sc... CSV
#> EH3901 scpdata/do... ftp://mass... XLS/XLSX
#> EH3902 scpdata/do... ftp://mass... XLS/XLSX
#> EH3903 scpdata/do... ftp://mass... XLS/XLSX
#> ... ... ... ...
#> EH9450 scpdata/gr... https://ww... TXT
#> EH9477 scpdata/kh... https://dr... TXT
#> EH9487 scpdata/gu... ftp://mass... TXT
#> EH9497 scpdata/pe... https://da... TXT
#> EH9498 scpdata/pe... https://da... TXT
## Load data using the ExperimentHub interface
hub <- ExperimentHub()
if (FALSE) {
## Download the data set of interest using ExperimentHub indexing
hub[["EH7711"]]
## Download the same data set using the build-in function
leduc2022()
}