Steffen Neumann

Hi, the above structure `library (group) ...` looks a lot like mzML to me. In fact, the OpenMS people already have a tool to search spectra in one mzML file...

Over the last weeks I heard several comments offline from people asking about the current data model, not knowing the current state. Can we make a push to collect that...

Hi, can you open the Document in "Comment" Mode for all with the link ? That should allow "Suggest mode" editing. And or respond to the "request permission" notification I...

Indeed, this refers to these ones: https://github.com/Bioconductor/bioc_docker#maintained-by-laurent-gatto-lg390camacuk built at https://hub.docker.com/r/bioconductor/release_proteomics2/builds/ and typical build failures are https://cloud.docker.com/u/bioconductor/repository/registry-1.docker.io/bioconductor/release_proteomics2/builds/c6648224-4f0f-4012-92eb-b149d72937f4 Some errors to fix are: - [ ] `Warning: dependency ‘pathological’ is not available`...

Hi, thanks for checking back. Currently, if I do some jq on some input json, I get the result in the output box, and with a shared snippet I can...

Hi @bernt-matthias , @cbroeckl recently discovered issues installing xcms via conda, reported in https://github.com/sneumann/xcms/issues/775. Checking https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-xcms I see that the latest xcms would be 4.0.0 from BioC-3.18. Any way to...

Hi, thanks for reporting. Can you link to the conda recipe that needs fixing ? And open an issue there as well, and cross-link the two ? I am not...

Not asking for R-4.0.0, but instead it wants to install xcms-4.0.0 from BioC-3.18: https://bioconductor.org/packages/3.18/bioc/html/xcms.html So indeed would be due for some refresh. I vaguely have in mind that bioconcda and...

Hi, indeed, @michaelwenk and Rene have worked on MassBank3. In the new interface https://msbi.ipb-halle.de/MassBank/search?compound_name=CP-457920 we don't group yet, but that could be a future feature, if we knew how. At...

Hi, checkout the search: https://github.com/search?q=repo%3Asneumann%2Fxcms%20featureValues&type=code There are plenty of hits, and it depends what you are looking for. Generics are defined at https://github.com/sneumann/xcms/blob/08e16491b226dacc5536d3fa0296da16467aa058/R/AllGenerics.R#L838 The methods are implemented for multiple objects,...