Query

xQTLquery_gene()

Query basic information (including name, symbol, position and description, etc. ) of genes.

xQTLquery_geneAll()

Fetch details of all genes supported in GTEx.

xQTLquery_sampleBySampleId()

Query sample's details with samples' IDs.

xQTLquery_sampleByTissue()

Query sample's details with tissue name

xQTLquery_tissue()

Fetch all details of a specified tissue or all tissues

xQTLquery_varId()

Query variant in GTEx with variant ID or dbSNP ID

xQTLquery_varPos()

Query varints in GTEx using genome position.

EBIquery_allTerm()

EBIquery_allTerm

extractGeneInfo()

extract gene infor of specified genome from gencodeGeneInfoAllGranges

Download

xQTLdownload_egene()

Download details of eGenes (eQTL Genes) for a specified gene or a tissue.

xQTLdownload_eqtl()

Download significant or unsignificant eQTL associations of a tissue or across all tissues

xQTLdownload_eqtlAllAsso()

Download summary statistics of eQTL of a specified gene, variant, tissue or study.

xQTLdownload_eqtlAllAssoPos()

Download summary statistics of eQTL with genome position.

xQTLdownload_eqtlExp()

Download normalized expression of gene for a eQTL pair.

xQTLdownload_eqtlSig()

Download significant eQTL associations of a specified tissue or across all tissues.

xQTLdownload_exp()

Download normalized gene expression at the sample level in a specified tissue.

xQTLdownload_geneMedExp()

Download median expression of all samples for specified genes across tissues.

xQTLdownload_sgene()

Download details of sGenes (sQTL Genes) for a specified gene or a tissue.

xQTLdownload_sqtlExp()

Download normalized expression of intron for a sQTL pair.

xQTLdownload_sqtlSig()

Download significant sQTL associations of a tissue or across all tissues

retrieveLD()

Retrive SNP pairwise LD from locuscompare database.

retrieveLD_LDproxy()

Retrive SNP pairwise LD from LDlink database

Visualize

xQTLvisual_anno()

Visualizing annotated variants

xQTLvisual_enrich()

Visualizing enriched variants

xQTLvisual_eqtl()

Box plot with jittered points for showing number and significance of eQTL associations

xQTLvisual_eqtlExp()

Boxplot of normalized expression among genotypes for eQTL.

xQTLvisual_geneExpTissues()

Violin plot of distribution of the gene expression profiles among multiple tissues.

xQTLvisual_genesExp()

Density plot of expression profiles of the gene

xQTLvisual_locusCombine()

Generate a combined figure including locuszoom and locuscompare plot object.

xQTLvisual_locusCompare()

Dotplot of comparing regional signals between GWAS and xQTL.

xQTLvisual_locusZoom()

Locuszoom plot for visualizing regional signals relative to genomic position with a file of summary statistics

xQTLvisual_PNPlot()

P-N plot

xQTLvisual_qqPlot()

plot quantile-quantile plot with pvalue

xQTLvisual_qtlPropensity()

Visualization of QTL specificity among multiple cells/tissues.

xQTLvisual_sqtlExp()

Boxplot of normalized expression among genotypes for sQTL.

Analyze

xQTLanalyze_anno()

annotate variants with genome positon

xQTLanalyze_calLambda()

calculate genomic control inflation factor

xQTLanalyze_coloc()

Conduct colocalization analysis with trait genes generated from xQTLanalyze_getTraits

xQTLanalyze_coloc_diy()

conduct colocalization analysis with customized QTL data

xQTLanalyze_enrich()

variant enrichment analysis

xQTLanalyze_getSentinelSnp()

Detect sentinel SNPs in a given summary statistis dataset.

xQTLanalyze_getTraits()

Identify trait genes using sentinel SNPs generated from xQTLanalyze_getSentinelSnp

xQTLanalyze_propensity()

eQTL-specific analysis