Alexei Martsinkovskiy

I think there would likely have to be some analogous code added. For example something like: ``` if use_neuron: Neuron training code else: normal training code ``` The API seems...

Hi, I tried your code, however I'm getting chrom_sizes is not defined, as the variable does not seem to be declared anywhere.

> @LinearParadox When you run `computeCommunProb` by using the default setting of `population.size = FALSE`, the population size will not affect the results. Got it. What setting do you recommend...

I think I've deleted/migrated a lot of the stuff on the machine unfortunately. I can describe it: The job stops normally,and it properly outputs the adjacency list. Just for some...

The command I used was: macs3 hmmratac -b $n --outdir $DIR -n $name --cuttoff-analysis-only I did read the help, and it is a little helpful. However, I'm not quite sure...

Here is all it gives me: INFO @ 08 Sep 2023 07:23:41: [106 MB] #1 Read fragments from BAM file... INFO @ 08 Sep 2023 07:23:44: [140 MB] 1000000 fragments...

Hi there, Thanks for your quick response! Here it is!  My design formula is: ~0+condition+batch Code: ``` res sccomp_glm( formula_composition = ~0+condition+batch, .sample = orig.ident, .cell_group = General_Idents, bimodal_mean_variability_association...

I see, got it, thank you! My other question is what changed between the old and new version? Using the same formula (~condition+batch) i get different results. Was there an...

The main difference would be that in the previous case, only the epithelial cell box was colored red. Now every condition has the right bar colored in red. Edit: I...

> yes, there is a branch for it. > > https://github.com/stemangiola/sccomp/tree/allow-plot-when-no-factors-are-present-in-the-contrasts > > This should plot all contrasts, but in the pool request a user ask me to improve the...