flekschas / enhancer-gene-vis Goto Github PK

after npm start. Type a gene name, the local webserver will crash and show the following:

And add // eslint-disable-next-line to the section does not work. see

Thank you.

This is in the second para of the introduction

"However, enhancers are not always active in every cell type or state. Hence, in reality the looks more like below where Enhancer 1 is entirely inactive in Sample 1 while Sample 2 is inactive in Sample 3." Don't you mean, "Enhancer 2 is inactive in Sample 3"?

The table should list enhancer-gene connections and allow them to be sorted by ABC score and biosample.

The table should also link to other resources like dbSNP, gnomAD, haploreg

In this case the focus region is set to chr15:99271685 and it looks like the app does show it:

https://flekschas.github.io/enhancer-gene-vis/?dai=true&dal=indicator&darn=true&e=chr15.95784077&egce=number&egi=true&egp=false&eri=solid&f=chr15.99271685&g=&s=chr10.84580725&vs=pValue&vt=VF5-RDXWTxidGMJU7FeaxA&w=false

However, this is due to the start position being set to chr10:84580725, which forces the view to go all the way from chr10-chr15.

There should be a better way to avoid such issues. Maybe a pop element or modal warning that the focus area is (almost) outside or too small compared to the main the view?

It will be great if it can show a custom track, like the UCSC genome browser.

Updated:
My goal is to check whether SV break an enhancer or not. Currently, it is not easy to get the location of a certain SV (using a mouse pointer). Thank you.

although it has a custom default track already, another track to show where is the SV segment among this default track will show genes nearby, which is important to the SV.

As an SV may disrupt an enhancer, so it will great to make an (column of) enhancer-centred view, besides the gene-centred view.

I am trying to use the edit variants function to add a list of SNPs I would like to view but they are not appearing on the track. The track name appears but I cannot see or search for any of my variants. I am uploading a local .bed file in which I have chromosome number in column 1(do I need chr or just number?) SNP position in columns 2 and 3 (can start and end position be the same?), rs ID in column 4 and probability in columns 5 and 6. Do the line endings need to be in a particular format eg CR LF?