EBIquery_allTerm        Query supported terms (phenotypes, studies,
                        tissues) in eQTL catalogue
extractGeneInfo         Extract gene details from
                        gencodeGeneInfoAllGranges object
retrieveLD              Retrieve SNP pairwise LD from locuscompare
                        database
retrieveLD_LDproxy      Retrieve SNP pairwise LD from LDlink database
xQTL_export             Export expression object to a specified format
xQTLanalyze_coloc       Conduct colocalization analysis with trait
                        genes generated from 'xQTLanalyze_getTraits'
xQTLanalyze_coloc_diy   Conduct colocalization analysis with customized
                        QTL data
xQTLanalyze_getSentinelSnp
                        Detect sentinel SNPs for GWAS using summary
                        statistics data
xQTLanalyze_getTraits   Identify trait genes using sentinel SNPs
                        generated from 'xQTLanalyze_getSentinelSnp'
xQTLanno_calLambda      calculate genomic control inflation factor for
                        a QTL/GWAS summary statistics dataset.
xQTLanno_chippeak       enrichment analysis for GWAS / QTL signals in
                        functional elements, including enhancer,
                        promoter, CPG, and TFs
xQTLanno_genomic        annotate all signals in GWAS / QTL dataset by
                        genome location
xQTLdownload_egene      Download eGenes (eQTL Genes) for a specified
                        gene or a tissue
xQTLdownload_eqtlAllAsso
                        Download summary statistics data for eQTLs with
                        a specified gene, variant, tissue or study
xQTLdownload_eqtlAllAssoPos
                        Download summary statistics data for eQTLs with
                        genome positions.
xQTLdownload_eqtlExp    Download normalized expression for gene with a
                        variant-gene pair
xQTLdownload_exp        Download normalized gene expression at the
                        sample level for a specified tissue.
xQTLdownload_geneMedExp
                        Download median expressions for multiple genes
                        in a specified tissue
xQTLdownload_hqtl       Download summary statistics data of H3K4me1 and
                        H3K27ac histone QTL (hQTL) using a specified
                        location
xQTLdownload_hqtlmeta   Download metadata for H3K4me1 and H3K27ac
                        histone QTL (hQTL)
xQTLdownload_mQTL       Download summary statistics data of DNA
                        methylation QTL (mQTL) using CpG ID
xQTLdownload_mqtlmeta   Download metadata of DNA methylation QTL (mQTL)
xQTLdownload_sc         Download all sc-eQTL associations for a
                        specified gene
xQTLdownload_scSig      Download significant sc-eQTL associations for a
                        specified gene
xQTLdownload_sgene      Download details of sGenes (sQTL Genes) for a
                        specified gene or a tissue.
xQTLdownload_sqtlAllAsso
                        Download summary statistics data for sQTLs with
                        a specified gene or a tissue
xQTLdownload_sqtlExp    Download normalized PSI value of intron for a
                        sQTL pair
xQTLdownload_xqtlAllAsso
                        Download summary statistics of xQTL for a
                        specified gene, default:3'aQTL
xQTLquery_eqtl          Query multi-tissue eQTL metasoft results
xQTLquery_eqtlSig       Query significant eQTL associations for a
                        specified tissue or multiple tissues.
xQTLquery_gene          Query basic information for genes, including
                        name, symbol, position and description
xQTLquery_geneAll       Query all genes supported in GTEx
xQTLquery_sampleBySampleId
                        Query details of samples with GTEx IDs
xQTLquery_sampleByTissue
                        Query details of samples by tissue name
xQTLquery_sc            Query significant sc-eQTLs for a specified gene
xQTLquery_scInfo        Query metadata of sc-eQTLs
xQTLquery_sqtlSig       Query significant sQTL associations for a
                        tissue or multple tissues
xQTLquery_tissue        Query details for a specified tissue
xQTLquery_varId         Query variant with variant ID or dbSNP ID
xQTLquery_varPos        Query variants using genome position.
xQTLvisual_PZPlot       Compare P-values reported to P-values
                        calculated from Z statistics derived from the
                        reported beta and standard error.
xQTLvisual_anno         Visualize enrichment of variants derived from
                        'xQTLanno_genomic'
xQTLvisual_coloc        Heatmap plot of the LD-p-value relationship of
                        the eQTL
xQTLvisual_eqtl         Box plot with jittered points for showing
                        number and significance of eQTL associations
xQTLvisual_eqtlExp      Boxplot of normalized expression stratified by
                        genotypes for eQTL.
xQTLvisual_geneExpTissues
                        Violin plot of distribution of the gene
                        expression profiles among multiple tissues.
xQTLvisual_genoBox      Boxplot of values stratified by genotypes with
                        customized data
xQTLvisual_locusCombine
                        Generate a combined figure including locusZoom
                        and locuscompare plot
xQTLvisual_locusCompare
                        Dotplot of comparing regional signals between
                        GWAS and xQTL
xQTLvisual_locusZoom    Locuszoom plot for visualizing regional signals
                        relative to genomic position with summary
                        statistics data
xQTLvisual_manhattan    Manhattan plot for a GWAS summary statistics
                        dataset
xQTLvisual_qqPlot       Quantile-quantile plot with p-values from GWAS
                        summary statistics data
xQTLvisual_sqtl         Box plot with jittered points for showing
                        number and significance of sQTL associations
xQTLvisual_sqtlExp      Boxplot of normalized PSI stratified by
                        genotypes for sQTL.
