NEWS.md

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

tima

tima 2.11.0

• Added convenience function to change small parameters (#177)
• Added demo files download to the app
• Better packaging
• Improved documentation
• Fixed all CRAN warnings
• Fixed some edge cases in spectra import
• Reduced dependencies
• Reduced exports
• Removed CompoundDb dependency as it was causing too many issues
• Removed pak install and switched to r-universe
• Replaced internal functions by Spectra equivalents (#166)
• Shinylive version available at https://taxonomicallyinformedannotation.github.io/tima-shinylive
• Simplified install and vignettes
• Switched from base::lapply to purrr::map

tima 2.10.0

• Added alt text to vignettes
• Added the possibility to add internal libraries through the GUI (#159)
• Added the possibility to filter confident annotations only (#140)
• Added number of peaks in spectrum
• Brought back some older dependencies to be compatible with oldrel
• Changed package name, usethis update
• Clearer handling of SIRIUS scores (#146, #147)
• Exposed more parameters to the GUI (#159)
• Facilitated install, no need to clone the directory anymore
• Finally made it to the r-universe
• Fixed adducts and removed nitrogen rule
• Fixed number of matched peaks
• Improved imports
• Reduced warnings
• Updated benchmarking steps

tima 2.9.6

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

tima 2.9.5

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

tima 2.9.4

• Automated update
• Added an option to remove ties (#134)
• Added some details for SIRIUS, added manual workspace addition (#132)
• Additional preprocessing (reduction) of noisy spectra
• Dependencies update
• 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
• Updated R and Bioconductor versions

tima 2.9.3

• Allowed for SIRIUS jobs containing only summaries
• Allowed for underscores in job pattern
• Changed some default values (less stringent)
• Dependencies update
• Migrated app testing to shinytest2
• Removed further some inconsistent MS1 annotations
• Removed tests dependencies by default

tima 2.9.2

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

tima 2.9.1

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

tima 2.9.0

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

tima 2.8.2

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

tima 2.8.1

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

tima 2.8.0

• Added GUI prototype
• Started using renv

tima 2.7.4

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

tima 2.7.3

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

tima 2.7.2

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

tima 2.7.1

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

tima 2.7.0

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

tima 2.6.0

• Added Docker container
• Changed data architecture
• Minor fixes

tima 2.5.6

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

tima 2.5.5

• Automation and parameters improvement
• Minor fixes

tima 2.5.4

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

tima 2.5.3

• Imports improvements
• LOTUS update

tima 2.5.2

• Packaging improvements

tima 2.5.1

• Improved support for SIRIUS (with new summaries)

tima 2.5.0

• LOTUS update
• Minor fixes

tima 2.4.0

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

tima 2.3.0

• 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
• Improved tests code coverage
• Minor fixes
• Updated adducts

tima 2.2.2

• Additional benchmark figure (Candidates distribution)
• Minor fixes

tima 2.2.1

• Minor version name fixes

tima 2.2.0

• Added benchmark (here)
• Various fixes

tima 2.1.0

• Fixes, deletion of binary dependencies.

tima 2.0.0

• Initial version.

taxonomicallyinformedannotation/tima-r documentation built on Jan. 25, 2025, 12:43 p.m.