I’m in need of one of your published articles:
Role of non-coding sequence variants in cancer
I will much appreciate if you could kindly send me a pdf copy of your published article for personal reading.
I saw your paper "Structuring supplemental materials in support of reproducibility" and appreciate your points. I would love to see a forum (like GATK’s forum or StackOverflow) where each topic for a conversation thread is a single published paper. Then everyone who is trying to replicate results could post their questions and authors their answers for all to see. I think this would be much better than the current closed system of emailing the authors. I would love to see a day when a link to a forum is provided on papers, rather than the authors’ email addresses.Who would have the ability to make something like this get started and catch on? Do you know if they are thinking about funding a platform for something like this at the NIH?
with respect to "Who would have the ability to make something like this get started and catch on?"
with respect to "Do you know if they are thinking about funding a platform for something like this at the NIH?"
I have been using the Genboree exceRpt workflow, and loving it! It has saved me so much time! Your paper got me on to it, and I would like to use one of the figures (1) of the exceRpt pipeline in my PhD thesis. Am I right to contact you to request permission? Or should I be heading to Cell for this?
fine w/ me – just acknowledge us (see
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?
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.
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?
Is this what you are looking for?
Regarding your paper entitled "3V: cavity, channel and cleft volume calculator and extractor", which I read carefully.
I’ve a question for you. In the abstract, it is written the following:"It rapidly finds internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces,…", but I think you mean "two imaginary rolling-probe solvent-excluded surfaces" because after looking at your code, I haven’t seen any analytic SES formulation therein. I guess you are just using two probe spheres of distinct radii to account for cavities, not the analytic SES themselves. Am I right?
I am not certain about your use of the term "imaginary", but I would say my method is a "discrete approximation" to the SES. And because it is discrete (i.e. a 3D grid) one can simply subtract one grid from another. See attached figures.
With small grid sizes (0.2 A), I see very little discrepancy to the analytical solution.
Could you please refer me to the link where can I download the chromatin state maps of C.elegans in your modENCODE paper http://www.sciencemag.org/content/330/6012/1775
At modencode.org., I found chip-seq or chip-chip data but not chromatin states.