Albert Vilella

log with different loses

4

Hi, is there a log in MethylDackel that records how many reads/bases are lost to issues like reads being discordant, singletons, dupes, or bases being below Q-score threshold, etc.? Would...

paired-end mode calling

2

Hi, There is a new sample prep that generates read pairs where the CpG modification needs to be read for both reads in a pair. E.g. ``` ff = forward/forward...

discrepancy between MethylDackel and IGV PBAT-style data aligned with bwameth

11

Hi, I tried to used MethylDackel extract on a dataset aligned with bwameth which was prepped with a PBAT-style method, in the sense that the data aligns to the CTOT...

feature request: only search within a list of potential peptides

2

Hi, Would it be possible for AfDesign to design peptides that bind a certain structure/domain but to do so for a given length *and* within a list (fasta file) of...

Here is a working version of the "binder redesign" idea as posited on Twitter: http://github.com/avilella/utils/blob/master/af/design.ipynb I've tried it a few times and the results make me think that there is...

Update README.md

1

splitting Unifold and Unifold-jax

Integrating facets into Jamovi

5

I am a big fan of Jamovi and Facets (https://pair-code.github.io/facets/) and would love to see both integrated. Facets seems to be a javascript library so maybe Jamovi could integrate it...

Is there a way to highlight a set of genes in the MA Plot? E.g. given a set of genes, have a series of highlighted dots with the gene names...

correlation with Facebook ESM's log_likelihood

8

Hi all, I've tested progen2 on an antibody Fv for which we've also calculated Facebook's ESM log_likelihood stability values, and we see very little correlation between the two. I've tested...

are these results sensible?

3

I am trying NucleoATAC on datasets of a lab workflow similar to ATAC-seq but not quite, and I am wondering if the results I am getting make sense. Some samples...