README.md

In saritaupatil/AutoBAT: Automated Analysis of Basophil Activation Testing Flow Cytometry Data

AutoBAT

Overview

AutoBAT is a tool developed for flow cytometry analysis of basophil activation testing

• BATgate() analyzes flow cytometry fcs files from basophil activation tests
• BATmeasures() derives measures of basophil activation testing dose-response curves, including area-under-the-curve(AUC) and ED50

These tools were developed for use with data generated from basophil activation testing. This data is generated by stimulation with antigens to generate aa dose-response stimulation curve, and subsequent parameters for data acquisition by flow cytometry include forward scatter height and area, side scatter, CCR3 and CD63.

For transparency of analysis, reproducibility, and high-throughput use, these tools provide a algorithm for data-driven identification of basophils and a cutoff for basophil degranulation (CD63 upregulation). Subsequent derivation of basophil activation testing measures using BATmeasures can be used as part of a workflow or separately.

Additional information can be found in Patil, et.al., "Data-driven programmatic approach to analysis of basophil activation tests", Cytometry: Part B - Clinical Cytometry. 2018 Jul;94(4):667-673. doi: 10.1002/cyto.b.21537.

The package is also available as a docker instance: saritapatil/autobat:1.0

Installation

Currently, the most efficient installation is

# The development version from GitHub:
# install.packages("devtools")
devtools::install_github("saritaupatil/AutoBAT")

If you encounter a clear bug, please file a minimal reproducible example on github. Please contact with any questions or concerns.

saritaupatil/AutoBAT documentation built on May 29, 2019, 1:25 p.m.