Answers.Body: <p>If you have more than a dozen or even hundreds of regions that you want to compare you could check a companion tool of HiGlass called <strong><a href="http://hipiler.higlass.io" rel="nofollow noreferrer">HiPiler</a></strong>. HiPiler lets you arrange, cluster, and pile up to thousands of genomic regions. Take a look at this <a href="https://www.youtube.com/watch?v=qoLqje5OYKg" rel="nofollow noreferrer">5min video introduction</a> to see if the tool could help you to answer your questions.</p>
  
  <p>Disclaimer: I am the creator of HiPiler.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-19T20:42:24.850Z
Answers.LastActivityDate: 2017-11-19T20:42:24.850Z
Answers.UserDisplayName: F Lekschas
Answers.Body: <p>Depending on the genome you want, you may be able to use the <a href="http://chorogenome.ie-freiburg.mpg.de/" rel="nofollow noreferrer">chorogeneome navigator</a>, which is from some of my colleagues. This uses a number of public HiC datasets and allows you to view interactions.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-07-21T18:47:06.840Z
Answers.LastActivityDate: 2017-07-21T18:47:06.840Z
Answers.UserDisplayName: Devon Ryan
Answers.Body: <p>I would also recommend two very recent Hi-C visualization frameworks (with some public data available in both): <a href="http://higlass.io/" rel="noreferrer">HiGlass</a> and <a href="http://www.aidenlab.org/juicebox/" rel="noreferrer">JuiceBox</a>.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-18T00:38:46.793Z
Answers.Text: HiGlass has the result of 7 different TAD callers available. Example using `hg38` can be found here: http://higlass.io/app/?config=IPCHmdOQR4CDY2sqj5VJHQ 
  
  Another example using `hg19` is here: http://higlass.io/app/?config=OBa3x6FiQtSC5g8Mj6u0pQ
  
  The TAD calls are from Forcato et al. 2017.
Answers.UserDisplayName: juniper-
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-27T22:41:15.197Z
Answers.LastActivityDate: 2017-08-27T22:41:15.197Z
Answers.UserDisplayName: golobor
Body: <p>I have identified a genomic region (CpG island) that is enriched for a characteristic of interest in the vast majority of my samples.</p>
  
  <p>After viewing it in the UCSC genome browser, I have confirmed that it does not overlap any annotated gene promoters, gene bodies, or retrotransposons, but am convinced that it is functionally interacting with something long range.</p>
  
  <p>Is there a publicly available visualization tool where I can input my genomic region and get a list of topologically associated domains from 3C or other chromatin-chromatin interaction data?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-18T00:32:56.277Z
Comments.Text: What assembly is your genomic region of interest in?
Comments.UserDisplayName: juniper-
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-26T18:00:32.860Z
Comments.Text: The assembly I used was hg19/GRCh37
Comments.UserDisplayName: Ben D.
Tags: <software-recommendation><visualization>
Title: Visualization tools for 3C/Hi-C long-range interaction data?
ThreadText: # Visualization tools for 3C/Hi-C long-range interaction data?
  
  (Asked by: username_0 on 2017-07-21)
  
  I have identified a genomic region (CpG island) that is enriched for a characteristic of interest in the vast majority of my samples.
  
  After viewing it in the UCSC genome browser, I have confirmed that it does not overlap any annotated gene promoters, gene bodies, or retrotransposons, but am convinced that it is functionally interacting with something long range.
  
  Is there a publicly available visualization tool where I can input my genomic region and get a list of topologically associated domains from 3C or other chromatin-chromatin interaction data?
  
  **Tags:** software-recommendation, visualization
  
  > **Comments:**
  > **username_1**: What assembly is your genomic region of interest in?  
  > **username_0**: The assembly I used was hg19/GRCh37  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_4 on 2017-08-27. Score: 6 | Accepted answer
  
  I would also recommend two very recent Hi-C visualization frameworks (with some public data available in both): [HiGlass](http://higlass.io/) and [JuiceBox](http://www.aidenlab.org/juicebox/).
  
  > **Comments:**
  > **username_1**: HiGlass has the result of 7 different TAD callers available. Example using `hg38` can be found here: http://higlass.io/app/?config=IPCHmdOQR4CDY2sqj5VJHQ   Another example using `hg19` is here: http://higlass.io/app/?config=OBa3x6FiQtSC5g8Mj6u0pQ  The TAD calls are from Forcato et al. 2017.  
  
  ---
  
  ### Answer by username_2 on 2017-11-19. Score: 3
  
  If you have more than a dozen or even hundreds of regions that you want to compare you could check a companion tool of HiGlass called **[HiPiler](http://hipiler.higlass.io)**. HiPiler lets you arrange, cluster, and pile up to thousands of genomic regions. Take a look at this [5min video introduction](https://www.youtube.com/watch?v=qoLqje5OYKg) to see if the tool could help you to answer your questions.
  
  Disclaimer: I am the creator of HiPiler.
  
  
  ---
  
  ### Answer by username_3 on 2017-07-21. Score: 2
  
  Depending on the genome you want, you may be able to use the [chorogeneome navigator](http://chorogenome.ie-freiburg.mpg.de/), which is from some of my colleagues. This uses a number of public HiC datasets and allows you to view interactions.
  
  
  ---
  
  