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Single Cell Proteomics Data Package

This package contains standardized and annotated single-cell proteomics data.

Installation instruction

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("UCLouvain-CBIO/scpdata")

Loading a data set

The available datasets can be accessed through the ExperimentHub API. The list of available datasets can be retrieved as follows.

library(ExperimentHub)
eh <- ExperimentHub()
(datasets <- query(eh, "scpdata"))

The desired dataset, for example the specht2019v2 dataset, can be downloaded and accessed using either the bracket selection:

scp <- datasets[["EH????"]]

Or the data loading function:

scp <- specht2019v2(metadata = FALSE)

The data description and data collection procedures can be found in the corresponding helpfiles that can be accessed using for instance ?specht2019v2.

Available data sets

There are many sources of published singe-cell proteomics work. We collected the associated data that can be found under 3 different levels:

  • PSM data is the data obtained after running feature identification and quantification from the raw data. Rows are spectral features and columns are samples.
  • Peptide data is the expression data where rows are peptides and columns are samples
  • Protein data is the expression data where rows are proteins and columns are samples

The amount of processing of each type of data might differ from data set to data set. Please refer to the documentation and original papers for thorough description of the data processing.

Meta-information about the available datasets in scpdata can be fetched with the following command:

mcols(datasets)