Tarik Salameh
Tarik Salameh
You only provide a positive set. any set of coordinates will be accepted, but ideally this should be from either an experiment different from the one you're training for (it...
Positive set will reflect garbage-in-garbage-out philosophy. peakachu is intended to receive coordinates determined by another technology (chia pet, etc) in the same cell type. When we tried manually selecting 200...
Yes, we pooled ChIA-PET coordinates and allowed for a +/- 1 bin tolerance when determining matches.
I assume you mean an interaction list for training right? There are a couple options: 1. Find an orthogonal experiment (like ChIA-PET, HiChIP, PLAC-Seq, Trac-loop, capture Hi-C, STORM, FiSH ...)...
Adding to Xiaotao's answer, the bed files should be found in the folder specified by the -O option. The folder will be created if it didn't exist already. If there...
That makes sense. Both example files were derived from excel sheets from each publication's supplemental files, and not from GEO.
Thank you for reporting this. Based on the error message and traceback, my first guess for the source of this issue is that it is caused by differences in sklearn...
No problem :) Your output shows installs from several channels -- pypi, anaconda, etc. While conflicts between pip and conda are better managed now in the past, conda's dep management...
checking in, were you able to get things working?