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Changelog

Source: NEWS.md

Metabonaut 1.3

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 1.2.1

  • 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.