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TcellExTRECT in WGS #18

Open Francesc-Muyas opened 2 years ago

Francesc-Muyas commented 2 years ago

Dear Tcell ExTRECT team,

I have some whole-genome sequencing (WGS) data sequenced at a decent coverage (50x). Can I apply this tool to WGS data and get the t cell infiltration fractions?

Thanks for your help, Francesc Muyas

rbentham commented 2 years ago

Hi Francesc,

Sorry for the late reply, right now the package is only for WES data, we are working on applying it to WGS and hopefully will be able to provide an updated method soon.

Best, Bobby

Francesc-Muyas commented 2 years ago

That sounds fantastic!

pcharoentong commented 1 year ago

Dear Tcell ExTRECT team,

Do you have any update on applying the TcellExTRECT to WGS data? We are looking forward to try it with our clinical trial data of NSCLC (n~200). Thank you very much.

Best,

Kay

adeschen commented 8 months ago

Hi,

According to posted document, the method has been adapted to WGS: https://www.cancerresearchhorizons.com/sites/default/files/2023-03/T%20Cell%20ExTRECT%20-%20March%202023.pdf

Are you planning to distribute the WGS adapted version to the scientific community (Non-Commercial Academic License)?

Best, Astrid

prakash-balasubr commented 6 months ago

Dear all,

Greetings from KiTZ & DKFZ!

Could you tell us if there is any update in running TcellExTRECT on WGS Samples. Kindly let me know.

Many thanks and Best Wishes, G P Balasubramanian.