| adjust_pvalues | Adjust p-values and filter gene-SNP pairs based on the adjusted p-values. | 
| buildZINB | Build a ZINB model. | 
| callQTL | Identify single-cell eQTLs exclusively using scRNA-seq data. | 
| checkSNPList | Validate SNP IDs in the input genotype matrix. | 
| CPM_normalize | Normalize gene expression using CPM. | 
| createGeneLoc | Create a gene location data frame. | 
| createQTLObject | Create an eQTLObject for storing sc-eQTL analysis data. | 
| createSNPsLoc | Create SNP location dataframe. | 
| DataSet | Test Gene Expression Dataset | 
| DESeq_normalize | Normalize the gene expression matrix with DESeq2. | 
| draw_boxplot | Generate a boxplot of gene expression by SNP genotype. | 
| draw_histplot | Generate a histogram of gene expression by SNP genotype. | 
| draw_QTLplot | Create a combined violin-box-scatter plot. | 
| draw_violinplot | Generate a violin plot of gene expression by SNP genotype. | 
| eQTLObject-class | Class 'eQTLObject' The eQTLObject class is designed to store data related to eQTL analysis, including data lists, result data frames, and additional metadata such as classification, species, and grouping information. | 
| filterGeneSNP | Filter gene expression and genotype matrices by cell percentage thresholds. | 
| filter_by_abs_b | Filter a data frame of gene–SNP 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_filter_data-method | Access filtered data stored in an eQTLObject. | 
| get_model_info | Access model specification from an eQTLObject | 
| get_model_info-method | Access model specification from an eQTLObject | 
| get_raw_data | Access raw data stored in an eQTLObject. | 
| get_raw_data-method | Access raw data stored in an eQTLObject. | 
| get_result_info | Access eQTLs results from an eQTLObject. | 
| get_result_info-method | 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_biclassify_info-method | Access biclassification information from an eQTLObject. | 
| load_group_info | Access cell grouping information from an eQTLObject | 
| load_group_info-method | Access cell grouping information from an eQTLObject | 
| load_species_info | Access species information from an eQTLObject. | 
| load_species_info-method | 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_filter_data-method | Set filtered data in an eQTLObject. | 
| set_model_info | Set model specification in an eQTLObject | 
| set_model_info-method | Set model specification in an eQTLObject | 
| set_raw_data | Set raw data in an eQTLObject. | 
| set_raw_data-method | Set raw data in an eQTLObject. | 
| set_result_info | Set eQTL results in an eQTLObject. | 
| set_result_info-method | Set eQTL results in an eQTLObject. | 
| show-method | Show Method for eQTLObject Class | 
| testEQTL | Test Gene Expression Dataset | 
| testGene | Test Gene Expression Dataset | 
| testSeurat | Test Gene Expression Dataset | 
| testSNP | Test Gene Expression Dataset | 
| testSNP2 | Test Gene Expression Dataset | 
| TPM_normalize | Normalize the gene expression matrix with TPM | 
| visualizeQTL | Visualize eQTL results by gene-SNP pair across groups | 
| zinbModel | Zinb model fitting the gene expression matrix. |