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Hello, thank you for your such a great package. I have multiple bigwig files, I want to plot multiple bigwig files in one heatmap, but the **normalizeToMatrix** function can only accept one signal fil…
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Hi Michael and the team,
thanks a lot for the tool and for the recent update to 4.0.3. I am currently working with heavily 5mCG methylated DNA samples (in vitro methylation) and I was planning to a…
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Hi, I am testing the meffil workflow with a publicly available dataset to see if I get the same results. But, I am unable to find any DMPs. I was able to reproduce the results using minfi but not usin…
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Hi Weilong,
I've notice that _--no-discordant_ option is always on. What's the reason for not reporting discordant mapping? Is it possible to disable this option?
Best,
Amira
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So, I performed direct RNA sequencing on nanopore and got fast5 files for them. When I do tombo resquiggle, should me reference fasta file by DNA or RNA sequence in fasta?
For instance, if I sequen…
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Hello @alexg9010 . I do have an unbalanced number of replicates for my conditions. For example, one condition A has 5 replicates B - 3 and C - 4. Can methylKit handle these uneven numbers of replicat…
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I am trying to run the BSmooth.tstat command. My data is not WGBS. It is targeted methylation data (which may be the issue). I was following directions from an Agilent bulletin to use this program wit…
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I try to run the following code:
```
python2 epiGBS/RnBeads/rnbeads_analysis.py \
add_and_analysis \
-f ./output_DMP_Scabi/ref.fa \
-b ./output_DMP_Scabi/methylation.filtered.bed \
-sf Scabi.c…
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# Issue Report
I am currently working on analyzing RNA methylation modifications using DRS data and DNA methylation modifications using ONT data. However, I have encountered several questions that I …
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Users currently need to download files manually one by one and then switch to one of the analysis tabs to run a particular analysis of interest. Assuming that the GUI is intended for relatively non-te…