The goal of this package is to identify response to a stimulant in
CyTOF/Flow cytometry stimulation assays by labeling cells as responded
or not based on an unsupervised high dimensional approach. Starting from
the annotated cell populations either through automated clustering such
as FlowSOM or traditional cell gating, the primary function
HDStIM() follows a heuristic approach to label cells as
responding or non-responding.
For a combination of cell population and stimulation type (e.g.,
CD127+ T-helper cells and interferon-alpha), HDStIM()
starts by performing k-means clustering on the combined set of cells
from stimulated and unstimulated samples. K-means clustering is
performed on expression data of all the state markers combined. Upon
clustering using a contingency table, a Fisher’s exact test determines
the effect size and the statistical significance of partitioning. Cells
form the combinations that pass the Fisher’s exact test are labelled as
responding.
You can install the released version of stimcellselector from CRAN with:
install.packages("HDStIM")And the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("niaid/HDStIM")Rohit Farmer: rohit.farmer@nih.gov, rohit.farmer@gmail.com