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| Tool | Description |
|---|---|
| MaxQuant | A quantitative proteomics software package for mass spectrometry-based proteomics. Often paired with Andromeda search engine. |
| Novor Cloud | A fast, real-time de novo sequencing tool for peptides, available as a cloud service. |
| MSFragger | A mass spectrometry database search tool known for speed and open modification search capabilities. |
| pFind | A comprehensive database search engine for proteomics data. |
| Sage | Proteomics software for advanced search and post-processing, developed for large-scale data analysis. |
| mMass | Open-source software for annotation and interpretation of mass spectra. Link |
| MassHunter | Agilent's software suite for mass spectrometry data acquisition and analysis. |
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🧮 Isotope
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Data analysis Tools
| Tool | Description |
|---|---|
| IsoReader | An R package for reading and processing stable isotope data.importing and handling isotope ratio mass spectrometry data in structured workflows. Especially useful with continuous-flow IRMS. |
| mixSIAR | A Bayesian mixing model framework in R for estimating diet composition from stable isotope data. Flexible with covariates and hierarchical models. |
| IsotopeR | R-based tool for isotope data analysis, including quality checks, basic plotting, and statistical summaries. Good for quick explorations. |
| FRUITS | Food Reconstruction Using Isotopic Transferred Signals — a GUI-based Bayesian mixing model for dietary reconstruction with prior constraints. Link |
| Lyticos | A lesser-known tool aimed at visualizing and interpreting isotope data in archaeological contexts. Useful for exploring multi-isotope datasets. |
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🧮 Dating / Chronology
| Tool | Description |
|---|---|
| OxCal | Widely used for Bayesian calibration of radiocarbon dates. Website |
| BCal | An on-line Bayesian radiocarbon calibration tool |
| R package for the analysis of large collections of radiocarbon dates | |
An open-source application developed at CNRS: https://chronomodel.com/ |
🧰 🧰 Programming & General Tools
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