Feedback / EpiExplorer

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Here you can tell us how can we make EpiExplorer more useful to you. Feel free to suggest new features, datasets, visualizations or vote for features suggested by other users.

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Mouse mm10 genome

8 ár síðan • 0

Would it be possible to get the mouse mm10 genome available?

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methylation thresholds

11 ár síðan • updated by 11 ár síðan • 1

Dear Konstantin, I have a related question. I have been exporing the original methylation files and was wondering which thresholds does EpiExplorer use for read coverage and percentage of reads with methylation. In UCSC they recommend requiring at least 10 reads and they assign colors depending on what fraction of the reads is found to be methylated.

Thanks again,

Federico

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Add a profile plot similar to the neighborhood plots

13 ár síðan • 0

Add a profile how often certain positions inside the regions, such as the start, the middle and the end overlap with a certain property.

For example, a profile plot showing 5,10,15,11,6 for the overlap of set of regions with CGIs will show that the 5'end overlaps in 5%, the 1/4 point overlaps in 10%, the middle point overlaps in 15% etc and would be indicative that the middle of the regions tend to be more overlapping with CGIs than the ends.

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Help bubbles

Óþekktur 13 ár síðan • 0

Allow more help bubbles?

For datasets information, tissues, plots, computations and others

One of those

http://craigsworks.com/projects/qtip/

http://craigsworks.com/projects/qtip2

http://www.vegabit.com/jquery_bubble_popup_v2/

Visualization

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Would it be possible to also get the rat genome (rn5) availlable?

Óþekktur 12 ár síðan • updated by 11 ár síðan • 0

Dear EpiExplorers,

Would it be possible to also get the rat genome (rn5) availlable?

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Answer

12 ár síðan

Dear user,

If you are planning a larger rat project we would certainly consider contributing. If this is the case, please contact our corresponding authors with more details (http://genomebiology.com/2012/13/10/R96). Otherwise, in order to be worth setting things up, we would need serious user interest in this genome that we have not yet observed.

same start and end position

Óþekktur 9 ár síðan • 0

I am a new user. I performed targeted bisulfite sequencing on 2 groups of samples and subsequently analyzed the data with Methylkit in R. My output file is a list of CpGs significantly differentially methylated between the 2 groups, with the 3 columns as requested by the EpiExplorer program (chr, start, end). My data is at single CpG level, thus start and end positions are exactly the same. This gives an error when uploading the file: "