NEWS.md

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

timaR

timaR 2.9.7

• Adding possibility to add internal libraries through the GUI (#159)
• Adding number of peaks in spectrum
• Expose more parameters to the GUI (#159)
• Fix adducts and remove nitrogen rule
• Fix number of matched peaks
• Updated benchmarking steps

timaR 2.9.6

• Adding light-switch thanks to pkgdown 2.1.0.
• Attempt to simplify installation
• Fix library/adducts confusion (#123)
• Fix some incorrect adduct differences annotations
• Refactored adducts / neutral losses / dimers annotation to allow for more flexibility (#141, #144)

timaR 2.9.5

• Do not re-package if already the latest version
• SIRIUS 6 default and compatible (keeping SIRIUS 5 backward compatibility)
• Update to Massbank version 2024.06

timaR 2.9.4

• Automated update
• Added an option to remove ties (#134)
• Added some details for SIRIUS, add manual workspace addition (#132)
• Additional preprocessing (reduction) of noisy spectra
• Docker updates (#131)
• Handle cases when same (feature_id, mslevel) pairs are present within an MGF (#133)
• Improved documentation
• New working directory at $HOME/.tima
• Dependencies update
• Update R and Bioconductor versions

timaR 2.9.3

• Allow for SIRIUS jobs containing only summaries
• Allow for underscores in job pattern
• Change some default values (less stringent)
• Dependencies update
• Migrate app testing to shinytest2
• Remove further some inconsistent MS1 annotations
• Remove tests dependencies by default

timaR 2.9.2

• Add Nitrogen rule to filter out some annotations
• Better handling of partial downloads (#118)
• Dependencies update (mainly targets 1.5.1, will invalidate previous targets)
• Fix some port issues in Shiny (#122)
• Remove completely empty columns from final output to avoid confusion (#120)

timaR 2.9.1

• Add Waystation action
• Add structures from spectral libraries to SOP library (#113)
• Expose all parameters (#107, #108)
• Fix for Zenodo API
• HMDB structures support
• Optimize grep/gsub by adding perl=TRUE or fixed=TRUE
• Update to Massbank version 2023.11
• Update SIRIUS preparation (#74, #115)

timaR 2.9.0

• Added compounds names as parameter
• Added MassBank spectral library (#77)
• Allow files outside data/source (#89)
• Added RT library as annotation library (#86)
• Be less dependent of GNPS by default
• Better handling of download errors
• Fixed Docker mount path
• Improved naming (#91)
• Internal variables refactoring
• New adducts (#79, #80)
• Refactored adducts, clusters and neutral losses
• Refactored biological and chemical score
• Refactored RT matching (#76)
• Refactored Sirius scores (#92)
• Multiple Shiny fixes and tests addition (#60)
• Multiple fixes (#71, #81, #82)

timaR 2.8.2

• Change from pbmclapply to pblapply
• Added spectral entropy
• Added MS1 only possibility
• Added Fluorine adduct
• Fix empty chemical classes
• Fix not classified taxa
• renv removal
• Performance improvement by replacing the tidyverse by the fastverse (in progress)
• Github Actions improvement
• Documentation improvement
• Reduced warnings (CRAN and jscpd)

timaR 2.8.1

• Added retry parameter to get_organism_taxonomy_ott
• Dependencies update
• Replace extdata loading
• Moved /params and paths.yaml to /inst as more standard. (see https://r-pkgs.org/misc.html#other-directories)
• Adapted tests
• Performance improvement by replacing the tidyverse by the fastverse (in progress)
• Minor fixes

timaR 2.8.0

• Adding GUI prototype
• Started using renv

timaR 2.7.4

• ECMDB support
• Edges (mass and spectra-based) and components are generated if not present.
• Fix case when no GNPS job ID
• Re-introducing Classyfire support.
• Retention time matching additionally to MS2 if RT present in library
• Parameters refactoring
• Steps refactoring
• Further Targets improvements
• Clearer vocabulary
• Lot of fixes

timaR 2.7.3

• Targets implementation
• Parameters refactoring
• Improved calculations over redundant formulas
• Spectral matching update (see https://github.com/rformassspectrometry/MetaboAnnotation/issues/93)
• Minor fixes

timaR 2.7.2

• Benchmark update (including negative mode)
• Spectral comparison + intensity filtering update
• Switched r-base Docker image to bioconductor with ARM support
• Improved parameters documentation
• Minor fixes

timaR 2.7.1

• Added parallelization on process_spectra
• Added sqlite storing for spectra
• Added MONA helpers
• Improved testing time
• Improved code documentation
• Minor fixes

timaR 2.7.0

• Added MS2 annotation capability (kudos @jorainer for the awesome Spectra suite)
• Added HMDB helpers for both taxo and ISDB
• Minor fixes

timaR 2.6.0

• Added Docker container
• Changed data architecture
• Minor fixes

timaR 2.5.6

• Minor fixes
• Partial functions cleanup
• Dependencies removal (e.g. metabo-store)

timaR 2.5.5

• Minor fixes
• Automation and parameters improvement

timaR 2.5.4

• Minor fixes
• Metadata completion improvement
• Molecular formula and adducts formalism improvement

timaR 2.5.3

• Imports improvements
• LOTUS update

timaR 2.5.2

• Packaging improvements

timaR 2.5.1

• Improved support for SIRIUS (with new summaries)

timaR 2.5.0

• Minor fixes
• LOTUS update

timaR 2.4.0

• Minor fixes
• Improved output (#34)
• Added chemical names and xlogp to output (#33)
• Added support for case when no consensus is found (#30)

timaR 2.3.0

• Minor fixes
• Added support for annotation without MN (#28)
• Added support for multi tool annotations (#27)
• Added support for classical MN GNPS jobs (#25)
• Added support for new version of LOTUS
• General improvements for manual inputs
• Updated adducts
• Improved tests code coverage

timaR 2.2.2

• Minor fixes
• Additional benchmark figure (Candidates distribution)

timaR 2.2.1

• Minor version name fixes

timaR 2.2.0

• Various fixes
• Added benchmark (here)

timaR 2.1.0

• Fixes, deletion of binary dependencies.

timaR 2.0.0

• Initial version.

taxonomicallyinformedannotation/tima-r documentation built on July 17, 2024, 7:11 p.m.