Profilling of Peripheral Blood Mononuclear Cells using CyTOF

This data package contains a subset of the Bodenmiller et al, Nat Biotech 2012 dataset for testing single cell, high dimensional analysis and visualization methods.


CyTOF enables the profiling of up to 100 parameters at the single cell level. Bodenmiller et al published the profiling of Peripheral Blood Mononuclear Cells (PBMCs) using 9 phenotypic and 14 functional markers. PBMCS are stimulated with 12 treatments and treated with 8 doses of various inhibitors, then profiled using CyTOF. PBMCs are manually gated using the phenotypic markers, identifying 14 populations for which the activity of different signaling networks can be assessed using the functional markers. More details are available in Bodenmiller et al Nat Biotech 2012.

To assess the efficiency of high-dimensional data analysis and visualization algorithms, the samples corresponding to untreated PBMCs, either unstimulated or after stimulation with BCR/FcR-XL, PMA/Ionomycin or vanadate are made available as 2 datasets:

  • refMat the signal intensity for each of the 23 channels, for 15792 untreated cells
  • untreatedMat the signal intensity for each of the 23 channels, for 36144 cells after stimulation with BCR/FcR-XL, PMA/Ionomycin or vanadate

For each dataset there are 3 additional matrix:

  • refPhenotMat and untreatedPhenoMat the signal intensity for the 9 phenotypic channels
  • refFuncMat and untreatedFuncMat the signal intensity for the 14 functional channels
  • refAnnots and untreatedAnnots the source file, cell type assignement and stimulation (where appropriate)

Install it from github with:

devtools::install_github("yannabraham/bodenmiller")

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("bodenmiller")

0.1 by Yann Abraham, 2 years ago


https://github.com/yannabraham/bodenmiller


Report a bug at https://github.com/yannabraham/bodenmiller/issues


Browse source code at https://github.com/cran/bodenmiller


Authors: Yann Abraham [aut, cre], Bernd Bodenmiller [aut]


Documentation:   PDF Manual  


CC0 license


Suggests ggplot2, dplyr, reshape2, RColorBrewer, knitr, rmarkdown


Suggested by Radviz.


See at CRAN