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Changelog

Source: NEWS.md

Metabonaut 1.6

Changes in 1.6.2

  • Fix Docker image to lock packages installed from GitHub to a specific commit/version: MsIO (0.0.17), RmzTabM (0.99.1), RuSirius (1.0.4).
  • Use SpectriPy from Bioconductor 3.23 release branch.
  • Update installation and usage descriptions.
  • Fix typos and formatting errors in the Using and Creating Metabolomics Data Annotation Resources and expand some textual passages.
  • Fix typos and expand descriptions in the LC-MS/MS Data Annotation using R and Python vignette.
  • Fix typos, format and reformulate some descriptions in the mzTab-M file format: import-export of mzTab-M 2.1 files from SummarizedExperiment.
  • Fix typos and small formatting issues in the Normalization and feature selection with the notame package vignette.
  • Remove comments and complete partial sentences in the Dataset investigation: What to do when you get your data vignette.
  • Remove unfinished/placeholder sections from the Dataset Investigation and End-to-End vignettes.
  • Point the README to the versioned docker image tag, consistent with the installation instructions.

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.