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  • Computational Tools and Analysis Section

    Overview

    This section provides an indexed list of computational methods, software packages, scripts, and analytical tools utilised within bioarchaeological research as described in the Manual. Each listed tool includes a concise description, intended application, and links to relevant webpages and GitHub repositories, including specific guidance on usage, robustness, error analysis, and reliability criteria.

    Tools by Application

    Proteomics

    Lipid Analysis

    • MassHunter

      • Description: Software for acquiring and processing mass spectrometry data, tailored especially for gas chromatography (GC-MS, GC-FID).

      • Webpage: MassHunter Software

      • Reliability Criteria: Internal QC via blank subtraction and retention-time alignment.

    • Omnic

      • Description: Software suite for Fourier-transform infrared (FTIR) spectroscopy that can be used for lipid analysis and interpretation.

      • Webpage: ThermoFisher Scientific - Omnic

      • Reliability Criteria: Offers extensive data validation tools for robust spectral analysis.

    Microfossil Analysis

    • C


    Radiocarbon Dating

    • OxCal

      • Description: Calibration software for radiocarbon dating, widely used for converting radiocarbon years (BP) to calendar dates.

      • Webpage: OxCal Calibration Software

      • Instructions: Detailed workflows available in OxCal Online Manual

      • Reliability Criteria: Includes statistical tools to manage calibration uncertainties and evaluate date reliability.

    • rcarbon (R package)

      • Description: An R package for calibration and statistical analysis of radiocarbon dates.

      • Repository: GitHub/rcarbon

      • Instructions: Package documentation available online; supports reproducible data analysis workflows.

    Stable Isotope Analysis

    • IsoReader

      • Description: Software for standardized reading, processing, and managing stable isotope data.

      • Repository: GitHub/IsoReader

      • Instructions: Extensive documentation and examples provided in the repository.

    • MixSIAR

      • Description: Bayesian mixing model designed to analyze stable isotope data, useful for diet reconstruction studies.

      • Repository: GitHub/MixSIAR

      • Reliability Criteria: Model robustness checked via diagnostic statistics and sensitivity analysis.

    ZooMS Analysis

    • mMass

      • Description: Open-source mass spectrometry software for ZooMS data analysis.

      • Webpage: mMass

      • Repository: GitHub/mMass

      • Instructions: Protocols.io guide available here.

      • Reliability Criteria: Software supports detailed spectral analysis and robust species identification through peptide markers.

    General Guidelines for Computational Tools

    • GitHub Repositories:

      • Scripts used in data processing and analysis are archived and publicly accessible via GitHub. Repository details include commit histories and version control for reproducibility.

    • Instructions for Usage:

      • Each computational tool comes with clearly documented instructions. Usage protocols include required data formats, step-by-step execution guidance, and troubleshooting sections.

    • Robustness and Error Analysis:

      • Analytical scripts and software provide error handling and robustness checks, including internal quality controls, validation datasets, and repeat analyses for accuracy verification.

    • Reliability Criteria:

      • Tools have been selected based on peer-reviewed reliability, robustness of results, reproducibility, and community endorsement within bioarchaeological research contexts.

    This structured documentation supports the consistent use and rigorous application of computational methodologies within bioarchaeological investigations, fostering transparent and reproducible research practices.

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