HipDynamics

Summary

HipDynamics is a R based downstream live-imaging analysis for the Human Induced Pluripotent Stem Cell Initiative (HIPSCI). The analysis allows quantification of cell population dynamics after preliminary image analysis of live images by CellProfiler and incorporation of plate_result.txt files generated from standardised end-point assays by the Operetta.

Installation

HipDynamics comes with a preconfigured directory structure and settings. In order to install HipDynamics simply pull this git-repository and everything should be set up for you.

Settings

HipDynamics holds all configurable variables within the hipDynamics.R file.

1. The database login-in- and end-point details need to be specified.
2. The plate_result.txt files directory path should be assigned to path_PR.
3. Optional settings allow specifying different analysis-methods and data exports.

Go-time

In order to run HipDynamics you need to enter the R-shell type the following command (provided you are within HipDynamics' directory folder and all settings were specified):

source("hipDynamics.R")

Running the Example

In order for you to run the example, you need to download the example_data.sql mysql database file from Google Drive and import it to your mysql sever. HipDynamics will try to find the database on your localhost by default. Should you want to run your server non-locally you can configure the host variable in the hipDynamics.R file.

Dependencies

R libraries:

1. gplots
2. ggplot2
3. ggdendro
4. reshape
5. RMySQL

Acknowledgments

1. Amos Folarin
2. HIPSCI Group of the Wattlab