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Hello there,
I have a question about calculateDiffMeth() function in package MethylKit that I used it to do differential RRBS analysis but I am not so familiar with its deep theory.
Because I ju…
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Hello,
I was running `modkit dmr pair`. I got `finished, processed 695 sites successfully, 1760883 failed` output. What could be the reason so many sites failed to process?
OUTPUT:
```
> runni…
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Hi, thanks for the great project. I'm attempting to load the latest Unimod XML file into Postgres using pyteomics and have encountered a few errors that I've attempted to solve along the way. I've doc…
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~Related to https://github.com/biothings/biothings_explorer/issues/880?~ Doesn't seem to be...
Noticing multiple cases in 10/20 automated test run, where edge-attributes were duplicated.
## Exa…
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Hello Yupeng,
There is an error for the latest version (1.4.7) installed from conda, failed to test DMRfind when running `python run_test.py`. See the following test output:
```
Tests start
Wed …
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Hi,
I did whole-genome bisulfite sequencing, and called methylation with MethylDackel.
I have 3 groups that I want to compare, and I want to use the most robust method to call differentially methyl…
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Hello there,
I have a question about dmrseq() function in this package.
There are 5 groups and more than 2 replicates in each group. I have idea that if dmrseq() can compare single sample betw…
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Hello, I am trying to run your code for "predicting new data" part. I follow all your command from creating new environment, install the requirement based on your txt file, until running the bash scri…
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Hi,
Are the DMR/DML outputs' columns pval type? For example, when analysing should we consider diff.Methy column as pval?
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Hi developers,
I hope this message finds you well. I have a quick question about the UCSCXenaShiny app in R. Is it possible to use human chromosome coordinates, like chr1:68044026-68054909, as a qu…