• 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

    • MaxQuant

      • Description: Comprehensive quantitative proteomics software suite designed for analysing large mass-spectrometry data.

      • Webpage: MaxQuant

      • Repository: GitHub/MqTools7

      • License: Freeware (proprietary but freely available)

      • Reliability Criteria: Robust peptide identification with built-in false discovery rate (FDR) assessment.

    • MetaMorpheus

      • Description: Software for high-throughput proteomics with enhanced sensitivity and comprehensive search capabilities.

      • Webpage: MetaMorpheus

      • Repository: GitHub/MetaMorpheus

      • License: Open-source (MIT License)

      • Documentation: 

    • Spectronaut

    • Scaffold

    • Comet

    • SPIN (Species by Proteome INvestigation) workflow

    Lipid Analysis

    Microfossil Analysis


    Radiocarbon Dating

    • OxCal

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

      • Webpage: OxCal Calibration Software

      • Documentation: Detailed workflows available in OxCal Online Manual

      • License: Freeware (free to use and distribute)

    • rcarbon (R package)

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

      • License: Open-source

      • Repository: GitHub/rcarbon

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

    • BCal

    • CALIB

      • License: Freeware (usage terms not specified)

      • Website: calib.org

    Stable Isotope Analysis

    • IsoReader

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

      • Repository: GitHub/IsoReader

      • License: Open-source (MIT License)

    • MixSIAR

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

      • Repository: GitHub/MixSIAR

      • License: Open-source (license not specified)

    • Escher-Trace

    • IsoSource

    • IsoError

      • License: Freeware (usage terms not specified)

      • Reference: EPA Resource

    ZooMS Analysis

    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.

    • R scripts

    • 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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