• How to contribute to text
• How to add packages

In the pdf seems something goes wrong with the figure captions. Some text ("1.bb") is added before caption.

From @nilshoffmann

The travis build still complains about this:
Package xcolor Warning: Incompatible color definition on input line 1816.
GitHub actions is just complaining about deprecation in https://github.com/rformassspectrometry/metaRbolomics-book/runs/2167721661?check_suite_focus=true#step:6:834

Please consider adding Integrated Probabilistic Annotation (IPA) - A Bayesian annotation method for LC/MS data integrating biochemical relations, isotope patterns and adduct formation

Reference https://doi.org/10.1021/acs.analchem.9b02354
Available from https://github.com/francescodc87/IPA

Can be set withrmd_subdir.

Latex errors when I add what should work:
urlcolor: blue
-->
! Package xcolor Error: Undefined color 'Maroon'.

Find how to auto label and how to cross reference.

by importing https://github.com/sneumann/metaRbolomics/blob/master/connectivity/packages.Rmd
as appendix. And/or run that in the preface of the book, so that the numbers are available
as R variables throughout the book. Yours, Steffen

Implementation started here: https://github.com/sneumann/metaRbolomics-book
Probably would be good with a dedicated docker as discussed here: #23

can you search for font in word?
also sub and superscripts need to be found.

Instead of many issues we can collect packages here as we find them.

• https://bioconductor.org/packages/release/bioc/html/statTarget.html
• http://mrr.sourceforge.net/download.html + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5029791/
• MolNetEnhancer
• Lipid Mini-On
• genuMet?
• Miodin
• trackViewer
• GMSimpute
• cmmr
• deisotoper
• see #26 https://github.com/wilsontom/metabolighteR + https://cran.r-project.org/web/packages/metabolighteR/index.html. Somewhere near Risa.
• AlpsNMR
• ChemoSpec2D
• Check https://github.com/yufree/xcmsrocker
• lipidomeR: https://www.biorxiv.org/content/10.1101/2020.03.16.994061v1 + https://lipidomer.org/
• Rmet
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5491020/ + https://github.com/salernos/RRmix
• https://github.com/NBDZ/dbnorm
• https://github.com/eMetaboHUB/MS-CleanR
• depict
• http://bioconductor.org/packages/3.12/bioc/html/POMA.html
• https://github.com/bachi55/rcdkTools
• TidyMass https://www.nature.com/articles/s41467-022-32155-w
• MobilityTransformR: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btac441/6628580?redirectedFrom=fulltext&login=false
• https://krispir.github.io/cpc/index.html

some are missing for unknown reason

• Figure references in bookdown
• Create reference style with https://editor.citationstyles.org/visualEditor/ that creates the code in place.
• Copy exported bibtex file

Chapter 1, Sections 2.2, 2.3, 2.8, and Chapter 3 do not seem to use the same output format / section format than the "normal" sections.

Add Spectra and MsBackendMgf to section 2.1 and Spectra, MsCoreUtils, MsBackendMassbank and MsBackendHmdb to section 2.2.

Unless you want only packages published in scientific journals to be added @stanstrup

need to copy from word tables manually --> check which fail. --> manual fix

Hi,

PAPi was identified as being non-maintained/unresponsive and will be deprecated in the next BioC release. PAPi is described in the section 2.7.4 Pathway analysis. I am wondering if we should keep it for historical reasons or remove it from the metaRbolomics book.

Some of our references were explicitly to websites. We need to have those links.
Also, it would be great to have DOI or article links in the bibliography.

Hi, I would like to start / add something on best practices for semantic annotation of software packages. Looking especially for @egonw, but other input more than welcome.

We'd need to collect things we want to see annotated, and examples how this has been done elsewhere.

The Elixir https://bio.tools/ is already collecting packages. including Metabolomics in R or details on xcms. They have some automatism, but the xcms information is kinda outdated.

• We should link the bio.tools pages to our tables, so people can go there.
• We should find out if the bio.tools information can be provided from within the packages, see bio-tools/biotoolsRegistry#454
• We should check if metabolomics-related terminology is missing in EDAM
• We could file bug reports for those on github that have very poor bio.tools annotation.
• We could file bug reports for those on github that have not even github tags for their projects.
• Once we have more semantic information, we can see how to get that via bioschemas back into the BioC web pages

Yours,
Steffen

We need

https://rformassspectrometry.github.io/metaRbolomics-book/0100-introduction.html

Probably related to: rstudio/bookdown#733
But updating doesn't help.

https://github.com/wilsontom/metabolighteR
https://cran.r-project.org/web/packages/metabolighteR/index.html

Somewhere near Risa.

Yours, Steffen

• make google sheet world readable. Write by request. If that setup is possible.
• read google sheet from R. AFAIR there are several packages. Figure which is maintained.
• Write CSV to "pages" for people to have easy access to the data

Don't know exactly.

@nilshoffmann did some nice updates but the rendering has failed since.

It seems to be because the chrome package changed from chromium-l10n to chromium-browser.
I changed what apt-get installs but I am running into a myriad of issues. Before I spend more time on this perhaps someone that usually works with Linux knows what is going on? @sneumann

First I got complaints about path to chrome, then it seems to need some snap to actually run chrome but I have no idea what that is supposed to do and cannot get it working.

Looks like there is a bug in dpl that makes deploy fail if there is no gh-pages branch: https://travis-ci.community/t/file-exists-dir-s-mkdir-ruby-exception-when-the-deploy-branch-doesnt-exist/1143

I have create an empty branch and is retesting.