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  "Title": "A complete analysis of single cell subpopulations, from\nidentifying subpopulations to analysing their relationship\n(scGPS = single cell Global Predictions of Subpopulation)",
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  "Description": "The package implements two main algorithms to answer two\nkey questions: a SCORE (Stable Clustering at Optimal\nREsolution) to find subpopulations, followed by scGPS to\ninvestigate the relationships between subpopulations.",
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  "BugReports": "https://github.com/IMB-Computational-Genomics-Lab/scGPS/issues",
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  "Date/Publication": "2026-04-28 12:50:33 UTC",
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      "source": "vignette.Rmd",
      "filename": "vignette.html",
      "title": "scGPS introduction",
      "author": "Quan Nguyen and Michael Thompson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Installation instruction",
        "2. A simple workflow of the scGPS:",
        "2.1 Create scGPS objects",
        "2.2 Run prediction",
        "2.3 Summarise results",
        "3. A complete workflow of the scGPS:",
        "3.1 Identify clusters in a dataset using CORE",
        "3.2 Identify clusters in a dataset using SCORE (Stable Clustering at Optimal REsolution)",
        "3.3 Visualise all cluster results in all iterations",
        "3.4 Compare clustering results with other dimensional reduction methods (e.g., tSNE)",
        "3.5 Find gene markers and annotate clusters",
        "4. Relationship between clusters within one sample or between two samples",
        "4.1 Start the scGPS prediction to find relationship between clusters",
        "4.2 Display summary results for the prediction",
        "4.3 Plot the relationship between clusters in one sample",
        "4.3 Plot the relationship between clusters in two samples"
      ],
      "created": "2017-11-30 05:55:26",
      "modified": "2020-12-02 04:40:54",
      "commits": 60
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