DESCRIPTION

Package: MSstatsConvertLLM
Type: Package
Title: LLM-Driven Schema Inference and Conversion for MSstats
Version: 0.1.0
Authors@R:
    person("Devon", "Kohler", email = "kohler.d@northeastern.edu",
           role = c("aut", "cre"))
Description: Uses locally-hosted large language models (LLMs) to automatically
    map columns of arbitrary mass-spectrometry proteomics tool output onto the
    standardized MSstats analysis schema. The inferred mapping (and any
    discovered quality-control filters) is fed into the existing MSstatsConvert
    pipeline via LLMtoMSstatsFormat(), reducing the manual overhead of onboarding
    new input formats. Also provides a benchmarking harness for evaluating how
    accurately different local models and prompt strategies recover the correct
    schema mapping against curated ground truth.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Depends:
    R (>= 4.0)
Imports:
    data.table,
    ellmer,
    jsonlite,
    MSstatsConvert
Suggests:
    MSstats,
    ggplot2,
    stringr,
    testthat (>= 3.0.0)
biocViews: Proteomics, MassSpectrometry, Preprocessing, Software
RoxygenNote: 8.0.0
Roxygen: list(markdown = TRUE)
URL: https://github.com/devonjkohler/MSstatsConvertLLM
BugReports: https://github.com/devonjkohler/MSstatsConvertLLM/issues