Changes in version 1.5                         

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.

                         Changes in version 1.4                         

Changes in 1.4.0

  - Add Notame vignette.

                         Changes in version 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

                         Changes in version 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.

                         Changes in version 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.

                         Changes in version 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.