EBIquery_allTerm |
Query supported terms (phenotypes, studies, tissues) in eQTL catalogue |
extractGeneInfo |
Extract gene infor of specified genome from gencodeGeneInfoAllGranges |
retrieveLD |
Retrive SNP pairwise LD from locuscompare database. |
retrieveLD_LDproxy |
Retrive SNP pairwise LD from LDlink database |
xQTLanalyze_coloc |
Conduct colocalization analysis with trait genes generated from 'xQTLanalyze_getTraits' |
xQTLanalyze_coloc_diy |
conduct colocalization analysis with customized xQTL data |
xQTLanalyze_getSentinelSnp |
Detect sentinel SNPs in a given summary statistis dataset. |
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_enrich |
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 details of eGenes (eQTL Genes) for a specified gene or a tissue. |
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_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_sqtlAllAsso |
download summary statistics of sQTL of a specified gene in GTEx v8. |
xQTLdownload_sqtlExp |
Download normalized expression of intron for a sQTL pair. |
xQTLdownload_xqtlAllAsso |
Download summary statistics of xQTL of a specified gene in GTEx v8, default:3'aQTL |
xQTLquery_eqtl |
query multi-tissue eQTL metasoft results |
xQTLquery_eqtlSig |
Download significant eQTL associations of a specified 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_sqtlSig |
Download significant sQTL associations of a tissue or across all tissues |
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_anno |
Visualizing annotated variants |
xQTLvisual_coloc |
heatmap of LD-p-value of the QTL |
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_manhattan |
Advanced CM plot of 11 |
xQTLvisual_PZPlot |
Compare P-values reported in the association result file to P-values calculated from Z statistics derived from the reported beta and standard error. |
xQTLvisual_qqPlot |
plot quantile-quantile plot with pvalue |
xQTLvisual_sqtl |
Box plot with jittered points for showing number and significance of sQTL associations |
xQTLvisual_sqtlExp |
Boxplot of normalized expression among genotypes for sQTL. |