William Kumler

One `xml_text` example includes the following comment: ``` #' # xml_double() and xml_integer() are useful for extracting numeric attributes ``` However, this text was previously spread across two lines: ```...

Too-long column names cause Shiny render to fail silently

6

Hi, super neat package you've got here and one I've found invaluable for data exploration and visualization. I ran into a super strange bug by trying to embed a heatmaply...

squallms

11

Update the following URL to point to the GitHub repository of the package you wish to submit to _Bioconductor_ - Repository: https://github.com/wkumler/squallms Confirm the following by editing each check box...

Best way to document additional XCMS object processing steps in the ProcessHistory slot?

3

Hi again, I'm writing a package that extends the default XCMS functionality with the option to return an XCMSnExp (and soon, hopefully, an XcmsExperiment object!) where low-quality features have been...

Move data.table to Depends instead of Imports?

1

Given that RaMS returns data.tables and I often then use data.table functions on them, it may make sense to automatically attach the data.table functions. Of course, this is very rarely...

mzXML files can have multiple binary encodings

2

The DDA file [from the Skyline folks in their DIA tutorial](https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dia) throws a bunch of warnings when run. Prying into these revealed that the mzXML file *sometimes* has an encoding...

Implement DBSCAN/OPTICS as an mz_group option?

1

Realized today that *m/z* group construction could be done with a 1D density-based clustering algorithm like DBSCAN or OPTICS. Perks of this would be that the "hard" *m/z* window currently...

#' See the package intro on GitHub at https://github.com/wkumler/RaMS and #' explore the vignettes with \code{vignette("help", package = "mypkg")}

Using opacityscale with surface results in ordering by addition order, not depth

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Hi all, been using plotly with R for a while now and really loving it - thanks for assembling such a phenomenal program! I'd like to report a bug found...

The new MS3 data file doesn't have homarine or GBT in it so the demo examples are useless :( not sure whether it's best to 1. switch back to the...