Gian M. Franceschini

icon indicating a website link https://gmfranceschini.simple.ink/

icon company University of Lausanne icon location Lausanne, Switzerland icon location Computational biologist in training, Cancer epigenomics Ph.D. in validation. Likely to overfit. Currently PostDoc at UNIL, Switzerland. Previously at UNITN.

Results 9 comments of Gian M. Franceschini

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Same issue with firefox via Snap

Does methyICC works for non-whole-blood tissues?

I have a similar issue so I post here and add a comment: in principle, I think you can modify the package to use `find_dmrs()` on something different from `flow.Sorted.Blood450k`....

Higashi stuck on training at higashi_model.train_for_imputation_nbr_0() on SLURM system

Unfortunately, it has not been solved so far.

Higashi stuck on training at higashi_model.train_for_imputation_nbr_0() on SLURM system

So, in the environment, I do: ``` export OMP_NUM_THREADS=1 ``` Then, I run the script, but it gets stuck as before with no additional info. Also, I tried to do:...

Higashi stuck on training at higashi_model.train_for_imputation_nbr_0() on SLURM system

If I can help you identify the problem somehow, please let me know. I'm happy to put some time into it.

Adding chromosome-wide prediction

Dear Jimin, I'd like to express also my interest for this feature. In the meantime, do you think there is any workaround I might experiment myself to get a chromosome...

Adding chromosome-wide prediction

Thank you for your answer @tanjimin, I think I got the idea. However, do you think it is possible to predict off-diagonal contacts as well? I mean with the aim...

Adding chromosome-wide prediction

Thanks a lot for your insights. I was indeed interested in compartment calling as the ultimate goal, but I see now that it is beyond the scope of your model.

NaNs in prediction.scores cause FindTransferAnchors to fail

After some additional investigation, we isolated the root of the problem in the result of `FindWeights()`. Apparently, the `k.weight` value, if too small, can cause the `prediction.scores` to be malformed....