RUCova: Removal of Unwanted Covariance in mass cytometry data

Mass cytometry data, cell area measurement data, and R Markdown reports to reproduce the figures of our publication and understand the application of RUCova.

Raw data were saved post de-convolution and spillover-compensation. Gates for singlets and non-dead cells (low_Pt) are included as logical columns and should be applied prior to usage.

Mass cytometry data sets:

• data1_HNSCC.csv -> Data from 10 Head-and-neck squamous cell carcinoma (HNSCC) cell lines in control condition and 48 h after irradiation with 10 Gy.
  • marker_category_HNSCC.csv -> table for each marker in the mass cytometry panel and category.
• data2_FACS.csv -> Data from Cal33 cell line under different stimuli and FACS-sorted by size (small and large).
  • size_gates.png -> Image depicting the FACS sorting.
• data3_ru.csv -> Data from Cal33 cell line with Ruthenium staining (Rapsomaniki et. al. 2018, doi: 10.1038/s41467-018-03005-5).
• data_ruthenium_rapsomaniki.csv (data from Rapsomaniki et. al. 2018) 

Cell area measurement data:

• cell_area_HNSCC.csv -> Measurements of the cell area [µm^2] via microscopy images for the 10 HNSCC in control condition and after irradiation with 10 Gy.

R Markdown reports:

• analysis.Rmd 
• analysis.html