ClinTAD | About
    Installation
  1. Python Installation
  2. ClinTAD Installation

  3. Getting Started
  4. Custom Tracks

  5. How It Works
  6. Basics
  7. Files Used
    1. TAD Boundary Files
    2. Human Phenotype Ontology File

    Citation
    Troubleshooting
    Planned features

Installation
1. Python Installation
In order to run ClinTAD locally, you must install Python. ClinTAD was developed using Python version 3.6.4, but most versions of Python 3 should work. When installing Python, please check the box to add Python to PATH.

2. ClinTAD Installation
The code for ClinTAD can be found on Github . Instructions(including a video tutorial) for local installation to be posted soon.

Getting Started
3. Custom Tracks
Once you have ClinTAD running locally, adding custom tracks is easy. Click on the Login button on the top right side of the website, create an account if needed, and login. Once you are logged in, click on your name in the top right and then click on the Tracks button in the dropdown menu. Fill out the Create New Track form, upload the file with your data, and click submit. The required file format is shown below with examples (columns are separated by tabs):

TADs
Chromosome Number Start Coordinate End Coordinate
1 1000000 2000000
1 2000000 3500000

CNVs and Enhancers
Chromosome Number Start Coordinate End Coordinate Element ID, Name, or Label Element Details
1 1000000 1009000 Element 1 Element 1 is a very important element!
1 2000000 2050000 Element 2 Element 2 is important for gene expression in several tissues!



How It Works
4. Basics
5. Files Used
a. TAD Boundary Files
The default TAD boundary file was provided by Jesse Dixon. The boundaries are derived from human embryonic stem cell data described in Chromatin architecture reorganization during stem cell differentiation, using the HG19 genome build, a bin size of 40kb, and a window size of 2Mb.

b. Human Phenotype Ontology File
The phenotype file used for this website is a modified version of the hp.obo file from Human Phenotype ontology, which was downloaded on December 2, 2017. Of note, the modified file used for this site is a list of combined ID fields and name fields from the original hp.obo file. Currently, the HPO Phenotype Lookup form only searches for matches between the input string and the hp.obo name field. Searching for matches in the "def" and "comment" field of the hp.obo file may be added in the future.

Citation
This tool was developed at the University of California San Francisco by Jacob Spector, MD and Arun Wiita, MD PhD.
Citation: to be posted soon

Troubleshooting
Problem: The Single tab is not loading or is causing the browser to crash.
Resolution: This can happen due to invalid inputs into one of the forms. Click the button below to clear the data, then try using the Single tab again.



Planned Features
1. Implement a Settings tab.
2. Allow for selection of what TAD boundary file to use. Currently, a default TAD boundary file in the HG19 build is used.
3. Add tracks
    a. CTCF binding sites
    b. CNV depletion (how frequent CNVs are at location)
    c. Benign and pathogenic CNVs