MOAT output

Q:
I have a problem with the analysis and I’m not sure if I am using you software properly. I am trying to calculate the mutation burden of some of my samples (similar to the measurements performed here: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0424-2#Sec2). I ended up trying to using MOAT from the second comment of this post in Biostars (https://www.biostars.org/p/299549/). However I cannot obtain the percentage as (nr.mutations/Mb). I am using MOAT-a using the argument “—wg_signal_mode=n”, I am doing something wrong?

A:
MOAT-a wasn’t meant to be used that way. The simulated variants in MOAT-a are internal data used to calculate p-value significance for elevated mutation burden on the input annotations. You can use MOAT-s to create a simulated variant set, and then calculate (number_of_mutations)/Mb from that.

source code for context-specific TF co-association analysis in ‘Architecture of the human regulatory network derived from ENCODE data’

Q:
I have benefited a lot from you work entitled ‘Architecture of the human regulatory network derived from ENCODE data’ and I want to use the framework you developed for context-specific TF co-association analysis. However, I can’t find the source code at your given address http://code.google.com/p/tf-co-association/. Do you have the replaced address to share the source code for that?

A:
Is this what you are looking for?
https://code.google.com/archive/p/tf-coassociation/source/default/source