Reference

Data retrieval
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_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.
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
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
Pre-processing
xQTLanno_calLambda()	Calculate genomic control inflation factor for a QTL/GWAS summary statistics dataset
xQTLanno_chippeak()	Annotate GWAS / QTL signals using bed4 format table object that provided by user
xQTLanno_genomic()	Genomic annotation of significant signals from GWAS / QTL
xQTL_export()	Export expression object to a specified format
Analyze
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
Visualize
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_genesExp()	Density plot of expression profiles for multiple genes
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_PZPlot()	Compare P-values reported to P-values calculated from Z statistics derived from the reported beta and standard error.
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.