Anand Mayakonda comments

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                                            Anand Mayakonda

methrix for ONT support

Hi Reka, I have an implementation of native support for ModKit bedMethyl files through a new `read_modkit()` function on the `modkit` branch. Initially, I tried implementing similar to how we...

methrix for ONT support

Hi Reka, Yes, I think it should be doable. Modkit's [bedMethyl tools](https://nanoporetech.github.io/modkit/intro_bedmethyl_merge.html) have nice options as well (merging similar mods).

methrix for ONT support

Hi Reka, Did you get a chance to test it? If this works for you, we can push it to Bioconductor for the upcoming October release.

methrix for ONT support

Hi, Thanks for testing. Could you please install again from modkit branch and try again? There were bunch of bugs with the tabix file streaming that caused the issue. I...

using a non-standard mouse genome build

Hi, build argument is only useful if you'd like to query UCSC for gene models. In your case, you should use a custom gtf file. Also set `query_ucsc = FALSE`...

using a non-standard mouse genome build

Hi, The attachment is missing. Could you please tray again?

Questions about MATH score

Hi, It does not account for CN changes.

Questions of GISTIC and copy number alteration analysis

Hi, Could you please post the commands used and the error?

Error in if (dist <= mergeDist) { : missing value where TRUE/FALSE needed

Hi, Unfortunately, `repel` is deprecated. Please do not use it. It will be removed soon.

track_plot issues

Hi, It's hard to guess the issue. Would it be possible to share the object `t`? Save it as an RDs file and attach it here.