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NEWS.md

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rgoslin 1.8.0

Please note that this Bioconductor version is based on Goslin version 2.2.0. See the Goslin repository and Goslin C++ repository for more details.

Improvements

  • Added more trivial mediators
  • Added prostglandins
  • Added oxylipins
  • Updated functional groups

Bug Fixes

  • Fixed oxo handling
  • Updated lipid class output for plasmanyl / plasmenyl to allow distinction

rgoslin 1.6.0

Please note that this Bioconductor version is based on Goslin version 2.0.0. See the Goslin repository and Goslin C++ repository for more details.

BioConductor 3.18 - Changes in 1.6.0

Improvements

  • Better handling of mediators
  • Translating gangliosides into new nomenclature structure
  • Updated HMDB grammar for parsing mediators in lipid names: e.g., PA(P-16:0/LTE4)
  • Parsing of adducts with heavy labeled isotopes now possible

Bug Fixes

  • Minor bug fixes
  • Removed wrong Lyso classification for SPB, SPBP, LHexCer, LSM

rgoslin 1.4.0

Please note that this Bioconductor version is based on Goslin version 2.0.0. See the Goslin repository and Goslin C++ repository for more details.

BioConductor 3.17 - Changes in 1.4.0

Improvements

  • Improved handling of Glycosphingolipids and carbohydrates
  • Improved headgroup normalization for Glycosphingolipids.
  • Added PMeOH.
  • Added TG-EST (estolide) Estolides [GL0305].
  • Added more sterol variants.

Bug Fixes

  • Fixed classification of SB1a as Sulfoglycosphingolipids (sulfatides) [SP0602].
  • Fixed classification of SHex2Cer as Sulfoglycosphingolipids (sulfatides) [SP0602].
  • Fixed classification of SMGDG as Glycosylalkylacylglycerols [GL0502], added synonym seminolipid.
  • Fixed classification of SQDG Glycosyldiacylglycerols [GL0501].
  • Fixed classification of sterols.

BioConductor 3.16 - Changes in 1.2.0

  • No noteworthy changes.

BioConductor 3.15 - Changes in 1.0.0

Improvements

  • Reduced memory consumption.
  • Added 'ChE' abbreviation.
  • Added FG hydroperoxy to mediator nomenclature, refinement of mediators.
  • Added more sphingosine and sphinganine synonyms.
  • Added more ether dialects to LipidMaps grammar.
  • Improved handling for SP without explicit OH description.
  • Added Sa So support.
  • Updated old SP shortcuts.
  • Added CholE as abbreviation for cholesterol esters.
  • Modifications and improvements for Windows.
  • Added column of elements to functional group list and class.
  • Added 'ChoE'.
  • Added functional group butylperoxy -> BOO.

Bug Fixes

  • Fixed handling of LIPID MAPS SP notation.
  • Fixed critical bug when parsing LIPID MAPS names.
  • Fixed implicit hydroxy count.
  • Fixed ACer rule for species level.
  • Fixed lcb rule in LipidMaps grammar.
  • Fixed S1P and Sa1P handling.
  • Fixed gangliosides in Goslin grammar.
  • Fixed correct handling of dummy FAs during sorting.
  • Fixed segmentation fault in FA parser event handler.

Changes in 0.99.1

  • The column names within the data frames returned from the parse* methods now use column names with dots instead of spaces. This makes it easier to use the column names unquoted within other R expressions.
  • All parse* methods now return data frames.
  • The Messages column has been added to capture parser messages. If parsing succeeds, this will contain NA and Normalized.Name will contain the normalized lipid shorthand name.
  • Parser implementations have been updated to reflect the latest lipid shorthand nomenclature changes. Please see the Goslin repository for more details.
  • Exceptions in the C++ part of the library are captured as warnings in R. However, if you parse multiple lipid names, exceptions will not stop the parsing process.