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### Description of feature
Hello,
Would it be possible not to instruct Bismark methylation extractor to use both the --comprehensive and --merge_non_CpG flags when specifying --comprehensive to t…
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I am struggling to understand, why the "Filter Option: Remove PCR duplicates” in the Genrich tool is set to "Yes" after running the MarkDuplicates tool with “If true do not write duplicates to the out…
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Hello,
I got the following error, and I cannot find .mango file in the output folder. Could you help me with this? Thank you!
$ hichipper --out raw-1h-rep1_out_hichipper --macs2-genome mm -mu co…
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In some cases the gene model files one uses for their analyses have chromosomes simply denoted as 1, 2,...X, Y instead of chr1, chr2, ..., chrX, chrY. I've run into this problem with SusScrofa 10.2 ge…
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Dear Authors,
We have been developing an R package called [Methrix](https://github.com/CompEpigen/methrix) for analyzing generic bedgrpah files from WGBS datasets. Data structure for storing summar…
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1. In the testis_data.pdf, it is stated that there are **37 DMRs** in 0.3nM PCB126 group. However, there are only **10 hypermethylated and 25 hypomethylated DMRs**. There seems to be a typo there. Ple…
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Hi,
I am trying to run this script and am successful to the point of "Generating spike normalized bedgraphs". At this point it doesn't seem to like my chrom_sizes file and it would be great if you…
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Hi,
Error pops up when I was running transAnalysis, it worked fine when I was creating my_obj and running near_bait analysis, any idea what went wrong here? Thanks!
> trans_results=transAnalysis(my…
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### Describe the bug, including details regarding any error messages, version, and platform.
Hi! I expected that R arrow package should pass checks on all CRAN machines, including
r-prerel-macos-ar…
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To enable `universe` creation, we will need to port [`uniwig`](https://github.com/databio/uniwig) over to this package and offer it up as a `cli`, a library crate interface, and ideally a python inter…