This is the community page for the EpiExplorer project. 

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. 


Bug reports are also eagerly anticipated, especially on Friday night


Tell us how to make it better. We'll listen

0

Methylation chart

Anonymous 7 years ago updated by Federico Abascal 7 years ago 3

Dear colleagues,

I am comparing a bed of exons against the corresponding full-genes bed file. By looking at  "DNA methylation (ENCODE)" I can see higher bars for full-genes (e.g. 75% unmethylated for genes compared to 5% unmethylated for exons). 


Below, it can be read: 

Chart description: The bar chart visualizes the percentage of regions in the selected region set that overlap with any of the listed genomic and epigenomic features on the x-axis.

And this is what I do not understand. The plot suggests more methylation on exons, but the chart description refers to percentages of regions that overlap with a given epigenomic feature. Then, if an exon intersects with a methylated region, then the corresponding gene should intersect too. What am I missing here?


Many thanks for EpiExplorer, it is really helpful,

Best,

Federico



0
Completed

Names of regions in "DNA methylation (BROAD)"

Anonymous 9 years ago updated by Halachev 9 years ago 0
The names of the region sets in section "DNA methylation (BROAD)" look ugly. It would be nicer if you use space instead of underline (like in all other region set names), and make the capitalization consistent.
Answer
Halachev 9 years ago

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User upload their own annotation data sets.

albrecht 9 years ago updated 9 years ago 0
Users to be able to upload not only custom BED files as annotation but also DNA methylation data, histone peaks and others
Datasets Feature Ideas
0

Custom DNA sequence patterns

Anonymous 9 years ago 0
Currently if DNA sequence is selected only the preselected basic sequence patterns are computed. Please, allow the user to specify custom DNA sequence patterns
0

Allow uploading to use as basis default or custom already processed attributes

Halachev 9 years ago updated 9 years ago 0
On the upload page currently it is allowed a new dataset to be specified either by pasting the bed data int he text area or uploading it in the file field. Add a third option to use as region set one of the default (or loaded custom ) datasets.
Visualization Datasets