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tima 2.11.0
- Added demo files download to the app
- Better packaging
- Improved documentation
- Fixed all CRAN warnings
- 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
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 2.8.0
- 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 2.7.2
- 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 2.5.1
- Improved support for SIRIUS (with new summaries)
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 2.2.0
- Added benchmark (here)
- Various fixes
tima 2.1.0
- Fixes, deletion of binary dependencies.
