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dieterich-lab / nmdtxdb

Shiny application and code for the database for NMD targets
https://shiny.dieterichlab.org/app/NMDtxDB
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Expanding dataset #2

Open tbrittoborges opened 1 year ago

tbrittoborges commented 1 year ago

Hi @boehmv,

I would like to comment and document on expanding the number of datasets. So far, I have processed data for phases 1 and 2 (all the cell types). These were systematically analyzed. The other datasets were not analyzed . I did try to figure out a way to quickly, for example, using a preprocessed server (such as recount3, among others), but this was impossible because the server misses most of the datasets.

What I have on my list:

Feel free to comment so we can update this. This is a "long-running" issue, meaning this will not be resolved in the short term, but we should aim to expand as much as we can.

CDieterich commented 1 year ago

Hi @tbrittoborges

I think we should add the Nanopore and Illumina data from https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02439-3#availability-of-data-and-materials