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      "title": "Calculate Amino Acid Composition (AAC) Descriptor",
      "topics": [
        "calculateAAC"
      ]
    },
    {
      "page": "calculateAutocor",
      "title": "Calculate Autocorrelation Descriptors",
      "topics": [
        "calculateAutocor"
      ]
    },
    {
      "page": "calculateBE",
      "title": "Tranform a Seqeuence into Binary Encoding (BE)",
      "topics": [
        "calculateBE"
      ]
    },
    {
      "page": "calculateCTDC",
      "title": "Calculate CTD Descriptors - Composition (C)",
      "topics": [
        "calculateCTDC"
      ]
    },
    {
      "page": "calculateCTDD",
      "title": "Calculate CTD Descriptors - Distribution (D)",
      "topics": [
        "calculateCTDD"
      ]
    },
    {
      "page": "calculateCTDT",
      "title": "Calculate CTD Descriptors - Transition (T)",
      "topics": [
        "calculateCTDT"
      ]
    },
    {
      "page": "calculateCTriad",
      "title": "Calculate Conjoint Triad Descriptor",
      "topics": [
        "calculateCTriad"
      ]
    },
    {
      "page": "calculateDC",
      "title": "Calculate Dipeptide Composition (DC) Descriptor",
      "topics": [
        "calculateDC"
      ]
    },
    {
      "page": "calculateF",
      "title": "Calculate F1 or F2 Descriptors",
      "topics": [
        "calculateF"
      ]
    },
    {
      "page": "calculateKSAAP",
      "title": "Calculate k-spaced Amino Acid Pairs (KSAAP) Descriptor",
      "topics": [
        "calculateKSAAP"
      ]
    },
    {
      "page": "calculateQD_Sm",
      "title": "Calculate Quadruples Composition (QC) Descriptor from Biochemical Similarity Classes",
      "topics": [
        "calculateQD_Sm"
      ]
    },
    {
      "page": "calculateTC",
      "title": "Calculate Tripeptide Composition (TC) Descriptor",
      "topics": [
        "calculateTC"
      ]
    },
    {
      "page": "calculateTC_Sm",
      "title": "Calculate Tripeptide Composition (TC) Descriptor from Biochemical Similarity Classes",
      "topics": [
        "calculateTC_Sm"
      ]
    },
    {
      "page": "corr_plot",
      "title": "Plot Correlation Matrix between Input Features",
      "topics": [
        "corr_plot"
      ]
    },
    {
      "page": "enrich.df",
      "title": "Enrichment Result",
      "topics": [
        "enrich.df"
      ]
    },
    {
      "page": "enrichfind_cpx",
      "title": "Functional Enrichment Analysis for Predicted Modules",
      "topics": [
        "enrichfind_cpx"
      ]
    },
    {
      "page": "enrichfind_hp",
      "title": "Functional Enrichment Analysis of all Host Proteins",
      "topics": [
        "enrichfind_hp"
      ]
    },
    {
      "page": "enrichfindP",
      "title": "Functional Enrichment Analysis for Pathogen Interactors in the High-Confidence Network.",
      "topics": [
        "enrichfindP"
      ]
    },
    {
      "page": "enrichplot",
      "title": "Plot the Enrichment Reuslt",
      "topics": [
        "enrichplot"
      ]
    },
    {
      "page": "example_data",
      "title": "Input Data for Prediction Algorithm",
      "topics": [
        "example_data"
      ]
    },
    {
      "page": "filter_missing_values",
      "title": "Drop the Missing Values Above a Certain Threshold",
      "topics": [
        "filter_missing_values"
      ]
    },
    {
      "page": "FreqInteractors",
      "title": "Plot the Pathogen Proteins' frequency of Interactions with Host Proteins",
      "topics": [
        "FreqInteractors"
      ]
    },
    {
      "page": "FSmethod",
      "title": "Feature Selection via Matrix Correlation and Recursive Feature Elimination (RFE)",
      "topics": [
        "FSmethod"
      ]
    },
    {
      "page": "get_negativePPI",
      "title": "Construct Negative Reference Host-Pathogen Protein-Protein Interactions (HP-PPIs)",
      "topics": [
        "get_negativePPI"
      ]
    },
    {
      "page": "get_positivePPI",
      "title": "Fetch Positive Reference Host-Pathogen Protein-Protein Interactions (HP-PPIs) from the BioGRID Database",
      "topics": [
        "get_positivePPI"
      ]
    },
    {
      "page": "getFASTA",
      "title": "Fetch FASTA Sequence from the UniProt Database",
      "topics": [
        "getFASTA"
      ]
    },
    {
      "page": "getHPI",
      "title": "Generating Host-Pathogen Protein-Protein Interaction (HP-PPI) Descriptors",
      "topics": [
        "getHPI"
      ]
    },
    {
      "page": "Gold_ReferenceSet",
      "title": "Gold-standard Reference Set of Inter-Species PPIs",
      "topics": [
        "Gold_ReferenceSet"
      ]
    },
    {
      "page": "host_se",
      "title": "Host SummarizedExperiment object",
      "topics": [
        "host_se"
      ]
    },
    {
      "page": "impute_missing_data",
      "title": "Impute missing Values per Features (i.e., Columns)",
      "topics": [
        "impute_missing_data"
      ]
    },
    {
      "page": "plotPPI",
      "title": "Plot the Predicted PPI",
      "topics": [
        "plotPPI"
      ]
    },
    {
      "page": "pred_ensembel",
      "title": "Predict Interactions via Ensemble Learning Method",
      "topics": [
        "pred_ensembel"
      ]
    },
    {
      "page": "predicted_PPIs",
      "title": "Predicted HP-PPIs",
      "topics": [
        "predicted_PPIs"
      ]
    },
    {
      "page": "run_clustering",
      "title": "Module Detection",
      "topics": [
        "run_clustering"
      ]
    },
    {
      "page": "unlabel_data",
      "title": "HP-PPIs with Unknown Class Labels",
      "topics": [
        "unlabel_data"
      ]
    },
    {
      "page": "UP000464024_df",
      "title": "Data.frame Containing SARS-CoV-2 FASTA Sequences",
      "topics": [
        "UP000464024_df"
      ]
    },
    {
      "page": "var_imp",
      "title": "Variable Importance Plot",
      "topics": [
        "var_imp"
      ]
    },
    {
      "page": "viral_se",
      "title": "Viral SummarizedExperiment object",
      "topics": [
        "viral_se"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/HPiP/raw/HEAD/README.md",
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  "_vignettes": [
    {
      "source": "HPiP_tutorial.Rmd",
      "filename": "HPiP_tutorial.html",
      "title": "Introduction to HPiP",
      "author": "Matineh Rahmatbakhsh",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overview of HPiP",
        "An Example of Predicting HP-PPIs",
        "Data Set Preparation",
        "Gold Standard Reference Dataset of Host-Pathogen PPIs",
        "FASTA Sequence extraction",
        "Sequence-based Features Extraction",
        "Amino acid Composition (AAC) Descriptor",
        "Dipeptide Composition (DC) Descriptor",
        "Tripeptide Composition (TC) Descriptor",
        "Tripeptide Composition (TC) from Biochemical Similarity Classes Descriptor",
        "Quadruplets Composition from Biochemical Similarity Classes Descriptor",
        "F1/F2 Composition Descriptor",
        "Composition/Transition/Distribution (CTD) Descriptors",
        "Composition (C) Descriptor",
        "Transition (T) Descriptor",
        "Distribution (D) Descriptor",
        "Conjoint Triad Descriptor",
        "Autocorrelation (Auto) Descriptors",
        "k-Spaced Amino Acid Pairs",
        "Binary encoding",
        "BString Object as Data Input",
        "Generate a SummarizedExperiment Objects",
        "Table of Summary Descriptors",
        "Combine Host-Pathogen Interaction Descriptors",
        "Data Processing",
        "Prediction Algorithm",
        "Nework Visualization",
        "GO Enrichment Analysis",
        "Complex Prediction",
        "Session info",
        "References"
      ],
      "created": "2021-09-10 18:27:05",
      "modified": "2025-11-23 20:13:33",
      "commits": 28
    }
  ],
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  "_indexed": true,
  "_nocasepkg": "hpip",
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