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Dataset for TiDEomics tutorial, expression matrix

Source: R/data.R
tutorial_data.Rd

A subset of GSE263759 data set published in Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation

Usage

data(tutorial_data)

Format

A data.frame with 500 rows and 41 variables:

Feature

Feature ID, e.g. gene symbols

Sample1, Sample2, ...

log2(CPM + 1) normalised expression values

Source

GSE263759

Details

Code for preparing the data is available in inst/script/tutorial_input.R

  • Ensembl IDs were mapped to symbols, genes with all zero counts were excluded.

  • Use time 0 untreated samples for other groups' time 0.

  • Include "untreated", "IFNbeta", "IFNgamma", "LPS" groups.

  • Sample 500 random genes.

  • Normalised to log2(CPM + 1).