scpdata: Single-Cell Proteomics Data Package

In UCLouvain-CBIO/scpdata: Single-Cell Proteomics Data Package

Single-Cell Proteomics Data Package

Description

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.

Usage

scpdata()

Value

A DataFrame table containing a summary of the available datasets.

Author(s)

Christophe Vanderaa

See Also

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

Examples

## List available datasets and their metadata 
scpdata()

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

## Not run: 
## Download the data set of interest using ExperimentHub indexing
hub[["EH7711"]]
## Download the same data set using the build-in function
leduc2022()

## End(Not run)

UCLouvain-CBIO/scpdata documentation built on Oct. 29, 2024, 4:22 p.m.