diff --git a/NEWS.md b/NEWS.md index ea74abf..bec16d3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,62 +1,69 @@ -# Version 1.0 +# SpectraTutorials 1.0 +## Changes in 1.0.1 + +- Add Zenodo doi to citation file and README. + +## Changes in 1.0.0 + +- Version published on https://doi.org/10.5281/zenodo.11210190 - Use R 4.4 and Bioconductor 3.19. -# Version 0.9 +# SpectraTutorials 0.9 -## Version 0.9.0 +## Changes in 0.9.0 - Use R 4.3 and Bioconductor 3.18. -# Version 0.8 +# SpectraTutorials 0.8 -## Version 0.8.2 +## Changes in 0.8.2 - Add second example why caching changes is better than saving to database. -## Version 0.8.1 +## Changes in 0.8.1 - Include feedback and suggestions from Philippine Louail. -## Version 0.8.0 +## Changes in 0.8.0 - Add new tutorial *`Spectra`: an expandable infrastructure to handle mass spectrometry data*. - Download MassBank data as an alternative from *AnnotationHub*. -# Version 0.7 +# SpectraTutorials 0.7 -## Version 0.7.3 +## Changes in 0.7.3 - Fix mislabeling columns as experimental spectra and rows as MassBank spectra in the spectra similarity matrix (thanks to CSAMA2023 attendee for pointing this out!). -## Version 0.7.2 +## Changes in 0.7.2 - Use `MsBackendSql` instead of `MsqlBackend`. -## Version 0.7.1 +## Changes in 0.7.1 - Simplify/clarify description of spectra data processing. -## Version 0.7.0 +## Changes in 0.7.0 - Add section on the use of the `MsqlBackend` and compare performance to `MsBackendMzR` and `MsBackendDataFrame`. -# Version 0.6 +# SpectraTutorials 0.6 -## Version 0.6.3 +## Changes in 0.6.3 - Better describe usage of the alternative SQLite MassBank database file in the two workshops. -## Version 0.6.2 +## Changes in 0.6.2 - Add citation. -## Version 0.6.1 +## Changes in 0.6.1 - Adapt to changes in `Spectra` >= 1.5.8: export `spectraVariableMapping` method. @@ -65,29 +72,29 @@ - Adapt to changes in `MetaboAnnotation` >= 0.99.4: also the ppm error is reported by `matchMz`. -## Version 0.6.0 +## Changes in 0.6.0 - Remove the `Spectra` object with data from HMDB. - Use a `CompDb` database for HMDB annotations. -# Version 0.5 +# SpectraTutorials 0.5 -## Version 0.5.0 +## Changes in 0.5.0 - Add additional vignette describing spectra matching with the `MetaboAnnotation` package and integration into an `xcms` analysis workflow. -# Version 0.4 +# SpectraTutorials 0.4 -## Version 0.4.0 +## Changes in 0.4.0 - Version used at the BioC2021 conference. - Use MassBank release 2021.03. - Restructure the document and simplify the analysis (reduce to mzML files with 20eV collision energy). -# Version 0.3 +# SpectraTutorials 0.3 -## Version 0.3.2 +## Changes in 0.3.2 - Use MassBank release 2021.02 and add expand descriptive text. diff --git a/README.md b/README.md index 103926e..6eebe7f 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,16 @@ respective workshop section. See [NEWS.md](NEWS.md) for information on the current version and a change log. +## Citation + +This tutorials (and future versions) are deposited at +[Zenodo](https://zenodo.org). To cite this version of the tutorial: + +Johannes Rainer and Philippine Louail. SpectraTutorials version 1.0.0: Mass +Spectrometry Data Analysis with Spectra. Zenodo, May +17, 2024. https://doi.org/10.5281/zenodo.11210190 + + ## Installation For on-line code evaluation the workshops can also be run using a self-contained diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 0000000..083fc1d --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,19 @@ +citHeader("To cite this workflow:") + +citEntry(entry = "Manual", + title = "SpectraTutorials: Mass Spectrometry Data Analysis with Spectra", + author = personList( + person(given = "Johannes", family = "Rainer"), + person(given = "Philippine", family = "Louail") + ), + publisher = "Zenodo", + year = "2024", + month = "may", + version = "v1.0.0", + doi = "10.5281/zenodo.11210190", + url = "https://doi.org/10.5281/zenodo.11210190", + textVersion = paste0("Johannes Rainer, & Philippine Louail. (2024). ", + "SpectraTutorials version 1.0.0: Mass ", + "Spectrometry Data Analysis with Spectra. ", + "Zenodo. https://doi.org/10.5281/zenodo.11210190") + )