CPM_normalize           Normalize gene expression using CPM.
DESeq_normalize         Normalize the gene expression matrix with
                        DESeq2.
DataSet                 The package includes five examplt datasets: a
                        gene expression matrix, two SNP genotype
                        matrices, a Seurat object, and an eQTL object.
TPM_normalize           Normalize the gene expression matrix with TPM
adjust_pvalues          Adjust p-values and filter SNP–gene pairs based
                        on the adjusted p-values.
buildZINB               Build a ZINB model.
callQTL                 Identify single-cell eQTLs.
checkSNPList            Validate SNP IDs in the input genotype matrix.
createGeneLoc           Create a gene location data frame.
createQTLObject         Create an eQTLObject for storing sc-eQTL
                        analysis data.
createSNPsLoc           Create SNP location dataframe.
draw_QTLplot            Create a combined violin-box-scatter plot.
draw_boxplot            Generate a boxplot of gene expression by SNP
                        genotype.
draw_histplot           Generate a histogram of gene expression by SNP
                        genotype.
draw_violinplot         Generate a violin plot of gene expression by
                        SNP genotype.
eQTLObject-class        Class 'eQTLObject'
filterGeneSNP           Filter gene expression and genotype matrices by
                        cell percentage thresholds.
filter_by_abs_b         Filter a data frame of SNP–gene pairs by
                        absolute beta.
get_cell_groups         Retrieve Cells by SNP Value
get_counts              Extract Counts from an Expression Matrix
get_filter_data         Access filtered data stored in an eQTLObject.
get_model_info          Access model specification from an eQTLObject
get_raw_data            Access raw data stored in an eQTLObject.
get_result_info         Access eQTLs results from an eQTLObject.
initialize_progress_bar
                        Progress Bar for Model Analysis.
limma_normalize         Normalize the gene expression matrix with limma
linearModel             Fit Linear Model for eQTL Mapping
load_biclassify_info    Access biclassification information from an
                        eQTLObject.
load_group_info         Access cell grouping information from an
                        eQTLObject
load_species_info       Access species information from an eQTLObject.
log_normalize           Normalize the gene expression matrix with
                        logNormalize method.
normalizeGene           Normalize gene expression data.
plots_theme_opts        Customized ggplot2 Theme for Plots
poissonModel            Poisson model fitting the gene expression
                        matrix and genotype matrix.
process_matrix          Process a matrix to extract a row and convert
                        it to a data frame.
remove_outliers         Remove outliers from gene expression data and
                        update cell groups.
set_filter_data         Set filtered data in an eQTLObject.
set_model_info          Set model specification in an eQTLObject
set_raw_data            Set raw data in an eQTLObject.
set_result_info         Set eQTL results in an eQTLObject.
visualizeQTL            Visualize eQTL results by SNP–gene pair across
                        groups
zinbModel               Zinb model fitting the gene expression matrix.
