Mass-Spectra Prediction Using the FIORA Model
Overview
Provides a wrapper for the python module 'FIORA' as well as a 'shiny'-App to facilitate data processing and visualization. 'FIORA' allows to predict Mass-Spectra based on the SMILES code of chemical compounds. It is described in the Nature Communications article by Nowatzky (2025) doi:10.1038/s41467-025-57422-4.
- several improvements regarding the shiny app
- plot output for spectra improved a lot, i.e. isomeric peaks are combined now, neutral losses are computed between fragments in addition to the precursor, annotation can be omitted for minor peaks, all sum formulas are depicted using subscript for numbers to improve readability, font size was increased
- Help page received some input (very basic, for first time users)
From NEWS.md in the release
Install
Health
ERRORtestsr-oldrel-macos-x86_64
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [30s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(fioRa)
>
> testthat::test_check("fioRa")
Saving _problems/test-fct_read_fiora-43.R
Loading required package: shiny
[ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (5): 'test-app_utils.R:40:1', 'test-app_utils.R:66:1',
'test-find_fiora_predict_paths.R:2:3', 'test-run_script.R:3:3',
'test-run_script.R:18:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-fct_read_fiora.R:43:3'): fioRa can read the standard fiora example annotated output mgf as Spectra format ──
Error in `verify_suggested(pkg = c("S4Vectors", "Spectra"))`: The use of this function requires package Spectra. Please install.
Backtrace:
▆
1. └─fioRa::read_fiora(fl = fl, fmt = "Spectra") at test-fct_read_fiora.R:43:3
2. └─fioRa:::convert2Spectra(out)
3. └─fioRa:::verify_suggested(pkg = c("S4Vectors", "Spectra"))
[ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
Error:
! Test failures.
Execution halted- ERROR12 OK, 1 ERRORNow
- ERROR10 OK, 4 ERROR2026-03-10
Documentation
- Help pages
- 5
- Examples that run
- 33%1 run in a plain check · 2 never run
- Exported functions with examples
- 75%
- Documented parameters
- 86%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Downloads
Repository
- PRs merged (all time)
- not measured
- Median days to close, 50 most recently updated closed issues
- 11
- Median days to close, 50 most recently updated closed PRs
- not measured
Stars over time
Forks over time
Issues over time
Commits over time
5 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/janlisec/fiora on 2026-10-22.
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Dependencies
Code & Tests
Datasets
People & History
Pick two releases to compare their code metrics.
- RR 4.6.0 released · 2026-04-24
- 0.3.7Latest
- 0.3.42025-11-11
- RR 4.5.0 released · 2025-04-11
Package metadata
- First published
- 2025-11-11
- Total releases
- 2 / 1 yrs
- License
- MIT + file LICENSE OSI
- Minimum R
- ≥ 3.5
- Bundled data
- 0.4 KB / 1 file
- Download size
- 56 KB
Cite
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