apiAdmin_ping | Heartbeat to check GTEx API server connectivity. |
apiEbi_ping | Heartbeat to check EBI API server connectivity. |
dbsnpQueryRange | retrieve snps from dbSNP using coordinate. |
EBIquery_allTerm | EBIquery_allTerm |
extractGeneInfo | extract gene infor of specified genome from gencodeGeneInfoAllGranges |
fetchContent | Fetch data using url by three methods |
fetchContentEbi | Fetch records from |
is.wholenumber | determine whether is a whole number: |
retrieveLD | Retrive SNP pairwise LD from locuscompare database. |
xQTLanalyze_coloc | Conduct colocalization analysis with trait genes generated from 'xQTLanalyze_getTraits' |
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 |
xQTLanalyze_TSExp | Perform tissue-specific expression analysis for genes. |
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 |
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. |
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_qtlPropensity | Visualization of QTL specificity among multiple cells/tissues. |
xQTLvisual_sqtlExp | Boxplot of normalized expression among genotypes for sQTL. |