Welcome

Welcome to the CellCyclePlot git repository. This Java application was developed to aid genome-wide interpretation of the logR and CN data. This applcation enables the user to scroll through the CN and LogR data of the cells of choice interactively.

The manuscript for this application is currently under the review and the acompanying dataset will be avaiable after the publication.

Download

You can download the applicaiton from the download page. Or, you can clone the repository. This application was developped using Processing.

Input files

To run the application, you will need 3 types of file: - LogR file - Copy number file - Configuration file

LogR file

LogR file is a tab separated text file, which consists of 5 columns:"Chr","Pos","logR","logRsegment", and "end". "Chr" is the chromosome id. "Pos" is the genomic position of the data on the chromosome. "LogR" is the raw LogR value at the position. "LogRsegment" is the segment value for that position, thus for a segment, the same value repeats for the same segment.

#!
Chr Pos logR    logRsegment end
1   1   -1.50420309856045   -0.495633171623038  730261
1   730262  -1.12325924264004   -0.495633171623038  820603
1   820604  -0.57727667225468   -0.495633171623038  875652 

Copy number file

Copy number file is similar to LogR file. The file is a tab separated text file, which consists of 5 columns:"Chr", "Pos", "rawCN", "segmentedCN", "end". Instead of "LogR" and "logRsegment", you have "rawCN" and "segmentedCN". The "segemtnedCN" value is an integer value.

#!
Chr Pos rawCN   segmentedCN end
1   1   0.859004415656909   1   730261
1   730262  0.92070070545861    1   820603
1   820604  1.81492262585811    1   875652

Configuration file

Configuration file is also a tab separated text file, which specifies the location of LogR files and Copy number files on your computer and additional information for your setting. One recommended way to prepare a configuration file is to use the GUI provided in the application. When you start up the application, it loads the data loading page, as shown below. Then, specify the nubmer of samples, and for each sample, give a it an unique name and select the LogR and Copy number files by clicking on "select" button. Please be aware that file url may vary depending on your operating system. Then, you can use the "Save the configuration" function to save the setting. When you click on "Save", you will be able to specify the folder or directory you want to save the configuration file. Because the configuration file is just a text file, you can also open and edit in a text editor of your choice.

Optional file

In addition, you can also provide a domain file, wich specifies the early and late replication domain segments.

Features

The application includes a number of interactive features. For a quick demonstration, please see the following video demonstration. Click here.

• Zooming and Panning
• Toggle to show and hide segment and raw data
• Toggle to show and hide some samples
• Toggle to show and hide domain information
• Drag and drop color box on to sample to change color
• Change the representation style: ellipse, dot and line
• Toggle to turn on and off stacking to show overlapping values in the copy number segments.
• Annotate a selected region and take a note for further analysis

Sample data

A sample dataset will be available upon the publication of the manuscript.

Publication

Coming soon.

Collaboration

• Niels Van dar Aa
• Parveen Dabas
• Thierry Voet

Development

• Ryo Sakai
• Jan Aerts

License

The MIT License (MIT). See the LICENSE.txt.