NEWS

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Metabonaut 1.6

Changes in 1.6.1

• Install RmzTabM in the docker image for the mzTab-M vignette.
• Document that Metabonaut can be run in the browser on the Bioconductor Workshop platform (workshop.bioconductor.org).

Changes in 1.6.0

• Add vignette to export and import MzTab-M files.

Metabonaut 1.5

Changes in 1.5.1

• Update the SpectriPy tutorial vignette to the current matchms API: the ModifiedCosine similarity was renamed to ModifiedCosineGreedy (tested with matchms 0.33.1). This is a pure renaming, the implementation was already greedy; the vignette now also mentions the exact ModifiedCosineHungarian alternative.

Changes in 1.5.0

• Add vignette for use and import of public mass spectral library data.
• Add pre-computed vignette for advanced feature annotation using RuSirius and SIRIUS.

Metabonaut 1.4

Changes in 1.4.0

• Add Notame vignette.

Metabonaut 1.3

Changes in 1.3.2

• Add export for GNPS2 integration to main vignette.
• Add summary plot for peakpicking results in main vignette.

Changes in 1.3.1

• Expand the Dataset investigation vignette with an example to define background and foreground MS signal.

• Fix CTR sample subsetting in the MS2 annotation part of the main vignette.

Changes in 1.3.0

• Update to Bioc 3.22

Metabonaut 1.2

Changes in 1.2.2

• Expand the Dataset investigation vignette with an example to define background and foreground MS signal.

Changes in 1.2.1

• Addition of libary(knitr) in end-to-end workflow.

Changes in 1.2.0

• Addition of a new vignette depicting a large scale processing using xcms. Due to its size, this is added as a pre-computed vignette to prevent re-knitting as much as possible.
• Docker image now based on the stable version of Bioconductor (3.21) instead of devel.

Metabonaut 1.1

Changes in 1.1.2

• Adding authors that have contributed to specific method/vignettes to the respective vignette's header.
• Update README.md to add the link to SpectriPy vignette.
• fix ORCID in description so it gets recognize as an ORCID.

Changes in 1.1.1

• Update docker to skip installation of R packages and caching of data files for the root user.
• Fix GHA to properly install all Python libraries during library(SpectriPy).

Changes in 1.1.0

• Add a vignette for combined R/Python data analysis using reticulate and SpectriPy.

Changes in 1.1.0

• Addition of a devel branch to the repository to maintain a stable version.

Changes in 1.0.1

• Minor fixes of DESCRIPTION and .yml
• Addition of a devel branch to the repository to maintain a stable version.

Changes in 1.0.0

• More plots in the data investigation vignette.
• In the main end to end vignette: added saving of the Spectra object with the significant features associated MS1 and MS2 data. To be used later by other vignettes.

Metabonaut 0.0

Changes in 0.0.7

• Fix typo and cut-off for MS2 annotation.
• Updated figure numbering.
• Added acknowledgment to community.
• added a figure in retention time alignment vignette.

Changes in 0.0.6

• Moving The PercentMissing filtering at the end of the pre-processing steps as it needs to be done before normalization.
• Addition of collapsing code to improve readability.
• Reduction of table size

Changes in 0.0.5

• Require MsIO version 0.0.8 to allow reading of stored MsBackendMetaboLights objects.
• Small updates and changes to the Seamless Alignment vignette:
  • simplify import of previously stored result object
  • avoid using the variable name param for every parameter object

Changes in 0.0.4

• Required alabaster.se.
• In the end-to-end vignette:
  • Removal of Spectra data in depth visualisation to move to the Data investigation vignette
  • Removal of internal standard matching to features in the Normalization part.
• Save an load lcms1 and res object from the end-to-end workflow to be used in the Seamless Alignment vignette. Using MsIO and alabaster.se

Changes in 0.0.3

• Require xcms version 4.3.4 and install the package from github.

Changes in 0.0.2

• Switch to Quarto instead of Rmarkdown
• Addition of Alignment to reference dataset vignette
• Addition of the Data investigation vignette
• Addition of the Install vignette

Changes in 0.0.1

• Addition of basic files for a workflow package.
• Addition of the end-to-end vignette.