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  "Title": "scQTLtools: an R/Bioconductor package for comprehensive\nidentification and visualization of single-cell eQTLs",
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  "Description": "scQTLtools is a comprehensive R/Bioconductor package that\nfacilitates end-to-end single-cell eQTL analysis, from\npreprocessing to visualization",
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  "Date/Publication": "2026-04-28 13:04:17 UTC",
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      "title": "The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.",
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      "title": "The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.",
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      "title": "The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.",
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      "file": "Seurat_obj.rda",
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      "title": "The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.",
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      "title": "The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.",
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      "title": "Build a ZINB model.",
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      "title": "Identify single-cell eQTLs.",
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    {
      "page": "checkSNPList",
      "title": "Validate SNP IDs in the input genotype matrix.",
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      "title": "Normalize gene expression using CPM.",
      "topics": [
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      "title": "The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.",
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        "EQTL_obj",
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    {
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      "title": "Generate a boxplot of gene expression by SNP genotype.",
      "topics": [
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    },
    {
      "page": "draw_histplot",
      "title": "Generate a histogram of gene expression by SNP genotype.",
      "topics": [
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    },
    {
      "page": "draw_QTLplot",
      "title": "Create a combined violin-box-scatter plot.",
      "topics": [
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    },
    {
      "page": "draw_violinplot",
      "title": "Generate a violin plot of gene expression by SNP genotype.",
      "topics": [
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    },
    {
      "page": "eQTLObject-class",
      "title": "Class 'eQTLObject'",
      "topics": [
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    },
    {
      "page": "filter_by_abs_b",
      "title": "Filter a data frame of SNP–gene pairs by absolute beta.",
      "topics": [
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    },
    {
      "page": "filterGeneSNP",
      "title": "Filter gene expression and genotype matrices by cell percentage thresholds.",
      "topics": [
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    },
    {
      "page": "get_cell_groups",
      "title": "Retrieve Cells by SNP Value",
      "topics": [
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    {
      "page": "get_counts",
      "title": "Extract Counts from an Expression Matrix",
      "topics": [
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    },
    {
      "page": "get_filter_data",
      "title": "Access filtered data stored in an eQTLObject.",
      "topics": [
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        "get_filter_data,eQTLObject-method"
      ]
    },
    {
      "page": "get_model_info",
      "title": "Access model specification from an eQTLObject",
      "topics": [
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        "get_model_info,eQTLObject-method"
      ]
    },
    {
      "page": "get_raw_data",
      "title": "Access raw data stored in an eQTLObject.",
      "topics": [
        "get_raw_data",
        "get_raw_data,eQTLObject-method"
      ]
    },
    {
      "page": "get_result_info",
      "title": "Access eQTLs results from an eQTLObject.",
      "topics": [
        "get_result_info",
        "get_result_info,eQTLObject-method"
      ]
    },
    {
      "page": "initialize_progress_bar",
      "title": "Progress Bar for Model Analysis.",
      "topics": [
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      ]
    },
    {
      "page": "limma_normalize",
      "title": "Normalize the gene expression matrix with limma",
      "topics": [
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    },
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      "title": "Fit Linear Model for eQTL Mapping",
      "topics": [
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    },
    {
      "page": "load_biclassify_info",
      "title": "Access biclassification information from an eQTLObject.",
      "topics": [
        "load_biclassify_info",
        "load_biclassify_info,eQTLObject-method"
      ]
    },
    {
      "page": "load_group_info",
      "title": "Access cell grouping information from an eQTLObject",
      "topics": [
        "load_group_info",
        "load_group_info,eQTLObject-method"
      ]
    },
    {
      "page": "load_species_info",
      "title": "Access species information from an eQTLObject.",
      "topics": [
        "load_species_info",
        "load_species_info,eQTLObject-method"
      ]
    },
    {
      "page": "log_normalize",
      "title": "Normalize the gene expression matrix with logNormalize method.",
      "topics": [
        "log_normalize"
      ]
    },
    {
      "page": "normalizeGene",
      "title": "Normalize gene expression data.",
      "topics": [
        "normalizeGene"
      ]
    },
    {
      "page": "plots_theme_opts",
      "title": "Customized ggplot2 Theme for Plots",
      "topics": [
        "plots_theme_opts"
      ]
    },
    {
      "page": "poissonModel",
      "title": "Poisson model fitting the gene expression matrix and genotype matrix.",
      "topics": [
        "poissonModel"
      ]
    },
    {
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