├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── GTExbiolinks.Rproj ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── analyze.R ├── anno.R ├── download.R ├── global.R ├── internal_dealWithGencode.R ├── query.R ├── sysdata.rda ├── visualize.R ├── xQTLbiolinks.R └── zzz.R ├── README.md ├── _pkgdown.yml ├── data ├── ebi_datasets.rda ├── ebi_study_tissues.rda ├── example_Coloc_colocResultAll.rda ├── example_Coloc_colocResultsig.rda ├── example_Coloc_gwasDF.rda ├── example_Coloc_hyprcolocResultAll.rda ├── example_Coloc_outGenes.rda ├── example_Coloc_sentinelSNP.rda ├── example_Coloc_traitsAll.rda ├── gencodeGeneInfoAllGranges.rda ├── gencodeGenetype.rda ├── sampleNum.rda ├── tissueSiteDetailGTExv7.rda └── tissueSiteDetailGTExv8.rda ├── docs ├── 404.html ├── LICENSE.html ├── articles │ ├── Colocalization_analysis_with_xQTLbiolinks.html │ ├── Quick_start.html │ ├── eQTL_Specificity.html │ ├── images │ │ ├── eqtl_spec.png │ │ ├── eqtl_specificity │ │ │ ├── heatmap_MMP7.png │ │ │ └── regression_MMP7.png │ │ ├── prostate │ │ │ ├── anno.png │ │ │ ├── prostate_Go.png │ │ │ ├── prostate_combined.png │ │ │ ├── prostate_cor.png │ │ │ ├── prostate_eQTL_exp.png │ │ │ ├── prostate_eqtlTissues.png │ │ │ ├── prostate_exp_multissues.png │ │ │ ├── prostate_geneExpInOneTissue.png │ │ │ ├── prostate_locuscompare.png │ │ │ ├── prostate_locuszoom_eqtl.png │ │ │ ├── prostate_locuszoom_gwas.png │ │ │ ├── qq_pz_plot.png │ │ │ └── venn_coloc_hyprcoloc.png │ │ ├── quick_start │ │ │ ├── QQplot.png │ │ │ ├── colocalization_framework.png │ │ │ ├── compare.png │ │ │ ├── eQTL_multiple_tissue.png │ │ │ ├── eqtl_legendF.png │ │ │ ├── exp.png │ │ │ ├── gwas_legendF.png │ │ │ ├── propensity.png │ │ │ └── xQTLvisual_locusCombine.png │ │ └── visualization │ │ │ ├── eQTLspecificity.png │ │ │ ├── geneExpTissues.png │ │ │ ├── visualization_locusCompare.png │ │ │ ├── visualization_locusZoom.png │ │ │ ├── visualization_locusZoom_eQTL1.png │ │ │ ├── visualization_locusZoom_eQTLpos.png │ │ │ ├── visualization_tissueExp.png │ │ │ ├── xQTLvisual_eqtl.png │ │ │ ├── xQTLvisual_eqtlExp.png │ │ │ ├── xQTLvisual_genesExp.png │ │ │ ├── xQTLvisual_locusCombine.png │ │ │ └── xQTLvisual_sqtlExp.png │ ├── index.html │ ├── query_download.html │ └── visualization.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── EBIquery_allTerm.html │ ├── Rplot001.png │ ├── apiAdmin_ping.html │ ├── apiEbi_ping.html │ ├── dbsnpQueryRange.html │ ├── ebi_datasets.html │ ├── ebi_qtl_groups.html │ ├── ebi_study_tissues.html │ ├── example_Coloc_colocResultAll.html │ ├── example_Coloc_colocResultsig.html │ ├── example_Coloc_gwasDF.html │ ├── example_Coloc_hyprcolocResultAll.html │ ├── example_Coloc_outGenes.html │ ├── example_Coloc_sentinelSNP.html │ ├── example_Coloc_traitsAll.html │ ├── extractGeneInfo.html │ ├── fetchContent.html │ ├── fetchContentEbi.html │ ├── gencodeGeneInfoAllGranges.html │ ├── gencodeGenetype.html │ ├── index.html │ ├── is.wholenumber.html │ ├── retrieveLD.html │ ├── retrieveLD_LDmatrix.html │ ├── retrieveLD_LDproxy.html │ ├── retrieveLD_LDproxy_old.html │ ├── sampleNum.html │ ├── tissueSiteDetailGTExv7.html │ ├── tissueSiteDetailGTExv8.html │ ├── xQTL_export.html │ ├── xQTLanalyze_TSExp.html │ ├── xQTLanalyze_anno.html │ ├── xQTLanalyze_calLambda.html │ ├── xQTLanalyze_coloc.html │ ├── xQTLanalyze_coloc_diy.html │ ├── xQTLanalyze_enrich.html │ ├── xQTLanalyze_getSentinelSnp.html │ ├── xQTLanalyze_getTraits.html │ ├── xQTLanalyze_propensity.html │ ├── xQTLanalyze_qtlSpecificity.html │ ├── xQTLanno_calLambda.html │ ├── xQTLanno_chippeak.html │ ├── xQTLanno_enrich.html │ ├── xQTLanno_genomic.html │ ├── xQTLbiolinks.html │ ├── xQTLdownload_egene.html │ ├── xQTLdownload_eqtl.html │ ├── xQTLdownload_eqtlAllAsso.html │ ├── xQTLdownload_eqtlAllAssoPos.html │ ├── xQTLdownload_eqtlExp.html │ ├── xQTLdownload_eqtlSig.html │ ├── xQTLdownload_exp.html │ ├── xQTLdownload_geneMedExp.html │ ├── xQTLdownload_hqtl.html │ ├── xQTLdownload_hqtlmeta.html │ ├── xQTLdownload_ld.html │ ├── xQTLdownload_mQTL.html │ ├── xQTLdownload_mqtlmeta.html │ ├── xQTLdownload_sc.html │ ├── xQTLdownload_scSig.html │ ├── xQTLdownload_sgene.html │ ├── xQTLdownload_sqtlAllAsso.html │ ├── xQTLdownload_sqtlExp.html │ ├── xQTLdownload_sqtlSig.html │ ├── xQTLdownload_xqtlAllAsso.html │ ├── xQTLquery_eqtl.html │ ├── xQTLquery_eqtlSig.html │ ├── xQTLquery_gene.html │ ├── xQTLquery_geneAll.html │ ├── xQTLquery_sampleBySampleId.html │ ├── xQTLquery_sampleByTissue.html │ ├── xQTLquery_sc.html │ ├── xQTLquery_scInfo.html │ ├── xQTLquery_sqtlSig.html │ ├── xQTLquery_tissue.html │ ├── xQTLquery_varId.html │ ├── xQTLquery_varPos.html │ ├── xQTLvisual_PNPlot.html │ ├── xQTLvisual_PZPlot.html │ ├── xQTLvisual_anno.html │ ├── xQTLvisual_coloc.html │ ├── xQTLvisual_enrich.html │ ├── xQTLvisual_eqtl.html │ ├── xQTLvisual_eqtlExp.html │ ├── xQTLvisual_geneCorr.html │ ├── xQTLvisual_geneExpTissues.html │ ├── xQTLvisual_genesExp.html │ ├── xQTLvisual_genoBox.html │ ├── xQTLvisual_locusCombine.html │ ├── xQTLvisual_locusCompare.html │ ├── xQTLvisual_locusZoom.html │ ├── xQTLvisual_manhattan.html │ ├── xQTLvisual_qqPlot.html │ ├── xQTLvisual_qtlPropensity.html │ ├── xQTLvisual_qtlSpecificity.html │ ├── xQTLvisual_sqtl.html │ └── xQTLvisual_sqtlExp.html └── sitemap.xml ├── img └── Overview.png ├── inst └── extdata │ ├── hg19ToHg38.over.chain │ └── sceQTL_study_info.txt ├── man ├── EBIquery_allTerm.Rd ├── apiAdmin_ping.Rd ├── apiEbi_ping.Rd ├── dbsnpQueryRange.Rd ├── ebi_datasets.Rd ├── ebi_study_tissues.Rd ├── example_Coloc_colocResultAll.Rd ├── example_Coloc_colocResultsig.Rd ├── example_Coloc_gwasDF.Rd ├── example_Coloc_hyprcolocResultAll.Rd ├── example_Coloc_outGenes.Rd ├── example_Coloc_sentinelSNP.Rd ├── example_Coloc_traitsAll.Rd ├── extractGeneInfo.Rd ├── fetchContent.Rd ├── fetchContentEbi.Rd ├── gencodeGeneInfoAllGranges.Rd ├── gencodeGenetype.Rd ├── is.wholenumber.Rd ├── retrieveLD.Rd ├── retrieveLD_LDproxy.Rd ├── sampleNum.Rd ├── tissueSiteDetailGTExv7.Rd ├── tissueSiteDetailGTExv8.Rd ├── xQTL_export.Rd ├── xQTLanalyze_coloc.Rd ├── xQTLanalyze_coloc_diy.Rd ├── xQTLanalyze_getSentinelSnp.Rd ├── xQTLanalyze_getTraits.Rd ├── xQTLanno_calLambda.Rd ├── xQTLanno_chippeak.Rd ├── xQTLanno_genomic.Rd ├── xQTLdownload_egene.Rd ├── xQTLdownload_eqtlAllAsso.Rd ├── xQTLdownload_eqtlAllAssoPos.Rd ├── xQTLdownload_eqtlExp.Rd ├── xQTLdownload_exp.Rd ├── xQTLdownload_geneMedExp.Rd ├── xQTLdownload_hqtl.Rd ├── xQTLdownload_hqtlmeta.Rd ├── xQTLdownload_mQTL.Rd ├── xQTLdownload_mqtlmeta.Rd ├── xQTLdownload_sc.Rd ├── xQTLdownload_scSig.Rd ├── xQTLdownload_sgene.Rd ├── xQTLdownload_sqtlAllAsso.Rd ├── xQTLdownload_sqtlExp.Rd ├── xQTLdownload_xqtlAllAsso.Rd ├── xQTLquery_eqtl.Rd ├── xQTLquery_eqtlSig.Rd ├── xQTLquery_gene.Rd ├── xQTLquery_geneAll.Rd ├── xQTLquery_sampleByTissue.Rd ├── xQTLquery_sc.Rd ├── xQTLquery_scInfo.Rd ├── xQTLquery_sqtlSig.Rd ├── xQTLquery_tissue.Rd ├── xQTLquery_varId.Rd ├── xQTLquery_varPos.Rd ├── xQTLvisual_PZPlot.Rd ├── xQTLvisual_anno.Rd ├── xQTLvisual_coloc.Rd ├── xQTLvisual_eqtl.Rd ├── xQTLvisual_eqtlExp.Rd ├── xQTLvisual_geneExpTissues.Rd ├── xQTLvisual_genesExp.Rd ├── xQTLvisual_genoBox.Rd ├── xQTLvisual_locusCombine.Rd ├── xQTLvisual_locusCompare.Rd ├── xQTLvisual_locusZoom.Rd ├── xQTLvisual_manhattan.Rd ├── xQTLvisual_qqPlot.Rd ├── xQTLvisual_sqtl.Rd └── xQTLvisual_sqtlExp.Rd └── vignettes ├── .gitignore ├── Colocalization_analysis_with_xQTLbiolinks.Rmd ├── Quick_start.Rmd ├── images ├── prostate │ ├── anno.png │ ├── prostate_Go.png │ ├── prostate_Go_old.png │ ├── prostate_combined.png │ ├── prostate_cor.png │ ├── prostate_eQTL_exp.png │ ├── prostate_eqtlTissues.png │ ├── prostate_exp_multissues.png │ ├── prostate_geneExpInOneTissue.png │ ├── prostate_locuscompare.png │ ├── prostate_locuszoom_eqtl.png │ ├── prostate_locuszoom_gwas.png │ ├── qq_plot_all.png │ ├── qq_pz_plot.png │ └── venn_coloc_hyprcoloc.png ├── quick_start │ ├── QQplot.png │ ├── colocalization_framework.png │ ├── compare.png │ ├── eQTL_multiple_tissue.png │ ├── eqtl_legendF.png │ ├── exp.png │ ├── gwas_legendF.png │ ├── propensity.png │ └── xQTLvisual_locusCombine.png └── visualization │ ├── eQTLspecificity.png │ ├── geneExpTissues.png │ ├── visualization_locusCompare.png │ ├── visualization_locusZoom.png │ ├── visualization_locusZoom_eQTL1.png │ ├── visualization_locusZoom_eQTLpos.png │ ├── visualization_tissueExp.png │ ├── xQTLvisual_eqtl.png │ ├── xQTLvisual_eqtlExp.png │ ├── xQTLvisual_genesExp.png │ ├── xQTLvisual_locusCombine.png │ └── xQTLvisual_sqtlExp.png ├── query_download.Rmd ├── references.bib └── visualization.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /GTExbiolinks.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/GTExbiolinks.Rproj -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/LICENSE.md -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/NEWS.md -------------------------------------------------------------------------------- /R/analyze.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/R/analyze.R -------------------------------------------------------------------------------- /R/anno.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/R/anno.R -------------------------------------------------------------------------------- /R/download.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/R/download.R -------------------------------------------------------------------------------- /R/global.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/R/global.R -------------------------------------------------------------------------------- /R/internal_dealWithGencode.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/R/internal_dealWithGencode.R -------------------------------------------------------------------------------- /R/query.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/R/query.R -------------------------------------------------------------------------------- /R/sysdata.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/R/sysdata.rda -------------------------------------------------------------------------------- /R/visualize.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/R/visualize.R -------------------------------------------------------------------------------- /R/xQTLbiolinks.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/R/xQTLbiolinks.R -------------------------------------------------------------------------------- /R/zzz.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/R/zzz.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/README.md -------------------------------------------------------------------------------- /_pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/_pkgdown.yml -------------------------------------------------------------------------------- /data/ebi_datasets.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/ebi_datasets.rda -------------------------------------------------------------------------------- /data/ebi_study_tissues.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/ebi_study_tissues.rda -------------------------------------------------------------------------------- /data/example_Coloc_colocResultAll.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/example_Coloc_colocResultAll.rda -------------------------------------------------------------------------------- /data/example_Coloc_colocResultsig.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/example_Coloc_colocResultsig.rda -------------------------------------------------------------------------------- /data/example_Coloc_gwasDF.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/example_Coloc_gwasDF.rda -------------------------------------------------------------------------------- /data/example_Coloc_hyprcolocResultAll.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/example_Coloc_hyprcolocResultAll.rda -------------------------------------------------------------------------------- /data/example_Coloc_outGenes.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/example_Coloc_outGenes.rda -------------------------------------------------------------------------------- /data/example_Coloc_sentinelSNP.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/example_Coloc_sentinelSNP.rda -------------------------------------------------------------------------------- /data/example_Coloc_traitsAll.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/example_Coloc_traitsAll.rda -------------------------------------------------------------------------------- /data/gencodeGeneInfoAllGranges.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/gencodeGeneInfoAllGranges.rda -------------------------------------------------------------------------------- /data/gencodeGenetype.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/gencodeGenetype.rda -------------------------------------------------------------------------------- /data/sampleNum.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/sampleNum.rda -------------------------------------------------------------------------------- /data/tissueSiteDetailGTExv7.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/tissueSiteDetailGTExv7.rda -------------------------------------------------------------------------------- /data/tissueSiteDetailGTExv8.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/data/tissueSiteDetailGTExv8.rda -------------------------------------------------------------------------------- /docs/404.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/404.html -------------------------------------------------------------------------------- /docs/LICENSE.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/LICENSE.html -------------------------------------------------------------------------------- /docs/articles/Colocalization_analysis_with_xQTLbiolinks.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/Colocalization_analysis_with_xQTLbiolinks.html -------------------------------------------------------------------------------- /docs/articles/Quick_start.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/Quick_start.html -------------------------------------------------------------------------------- /docs/articles/eQTL_Specificity.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/eQTL_Specificity.html -------------------------------------------------------------------------------- /docs/articles/images/eqtl_spec.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/eqtl_spec.png -------------------------------------------------------------------------------- /docs/articles/images/eqtl_specificity/heatmap_MMP7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/eqtl_specificity/heatmap_MMP7.png -------------------------------------------------------------------------------- /docs/articles/images/eqtl_specificity/regression_MMP7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/eqtl_specificity/regression_MMP7.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/anno.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/anno.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/prostate_Go.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/prostate_Go.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/prostate_combined.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/prostate_combined.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/prostate_cor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/prostate_cor.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/prostate_eQTL_exp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/prostate_eQTL_exp.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/prostate_eqtlTissues.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/prostate_eqtlTissues.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/prostate_exp_multissues.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/prostate_exp_multissues.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/prostate_geneExpInOneTissue.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/prostate_geneExpInOneTissue.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/prostate_locuscompare.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/prostate_locuscompare.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/prostate_locuszoom_eqtl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/prostate_locuszoom_eqtl.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/prostate_locuszoom_gwas.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/prostate_locuszoom_gwas.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/qq_pz_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/qq_pz_plot.png -------------------------------------------------------------------------------- /docs/articles/images/prostate/venn_coloc_hyprcoloc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/prostate/venn_coloc_hyprcoloc.png -------------------------------------------------------------------------------- /docs/articles/images/quick_start/QQplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/quick_start/QQplot.png -------------------------------------------------------------------------------- /docs/articles/images/quick_start/colocalization_framework.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/quick_start/colocalization_framework.png -------------------------------------------------------------------------------- /docs/articles/images/quick_start/compare.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/quick_start/compare.png -------------------------------------------------------------------------------- /docs/articles/images/quick_start/eQTL_multiple_tissue.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/quick_start/eQTL_multiple_tissue.png -------------------------------------------------------------------------------- /docs/articles/images/quick_start/eqtl_legendF.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/quick_start/eqtl_legendF.png -------------------------------------------------------------------------------- /docs/articles/images/quick_start/exp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/quick_start/exp.png -------------------------------------------------------------------------------- /docs/articles/images/quick_start/gwas_legendF.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/quick_start/gwas_legendF.png -------------------------------------------------------------------------------- /docs/articles/images/quick_start/propensity.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/quick_start/propensity.png -------------------------------------------------------------------------------- /docs/articles/images/quick_start/xQTLvisual_locusCombine.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/quick_start/xQTLvisual_locusCombine.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/eQTLspecificity.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/eQTLspecificity.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/geneExpTissues.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/geneExpTissues.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/visualization_locusCompare.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/visualization_locusCompare.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/visualization_locusZoom.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/visualization_locusZoom.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/visualization_locusZoom_eQTL1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/visualization_locusZoom_eQTL1.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/visualization_locusZoom_eQTLpos.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/visualization_locusZoom_eQTLpos.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/visualization_tissueExp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/visualization_tissueExp.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/xQTLvisual_eqtl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/xQTLvisual_eqtl.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/xQTLvisual_eqtlExp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/xQTLvisual_eqtlExp.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/xQTLvisual_genesExp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/xQTLvisual_genesExp.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/xQTLvisual_locusCombine.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/xQTLvisual_locusCombine.png -------------------------------------------------------------------------------- /docs/articles/images/visualization/xQTLvisual_sqtlExp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/images/visualization/xQTLvisual_sqtlExp.png -------------------------------------------------------------------------------- /docs/articles/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/index.html -------------------------------------------------------------------------------- /docs/articles/query_download.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/query_download.html -------------------------------------------------------------------------------- /docs/articles/visualization.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/articles/visualization.html -------------------------------------------------------------------------------- /docs/authors.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/authors.html -------------------------------------------------------------------------------- /docs/bootstrap-toc.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/bootstrap-toc.css -------------------------------------------------------------------------------- /docs/bootstrap-toc.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/bootstrap-toc.js -------------------------------------------------------------------------------- /docs/docsearch.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/docsearch.css -------------------------------------------------------------------------------- /docs/docsearch.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/docsearch.js -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/index.html -------------------------------------------------------------------------------- /docs/link.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/link.svg -------------------------------------------------------------------------------- /docs/news/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/news/index.html -------------------------------------------------------------------------------- /docs/pkgdown.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/pkgdown.css -------------------------------------------------------------------------------- /docs/pkgdown.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/pkgdown.js -------------------------------------------------------------------------------- /docs/pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/pkgdown.yml -------------------------------------------------------------------------------- /docs/reference/EBIquery_allTerm.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/EBIquery_allTerm.html -------------------------------------------------------------------------------- /docs/reference/Rplot001.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/Rplot001.png -------------------------------------------------------------------------------- /docs/reference/apiAdmin_ping.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/apiAdmin_ping.html -------------------------------------------------------------------------------- /docs/reference/apiEbi_ping.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/apiEbi_ping.html -------------------------------------------------------------------------------- /docs/reference/dbsnpQueryRange.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/dbsnpQueryRange.html -------------------------------------------------------------------------------- /docs/reference/ebi_datasets.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/ebi_datasets.html -------------------------------------------------------------------------------- /docs/reference/ebi_qtl_groups.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/ebi_qtl_groups.html -------------------------------------------------------------------------------- /docs/reference/ebi_study_tissues.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/ebi_study_tissues.html -------------------------------------------------------------------------------- /docs/reference/example_Coloc_colocResultAll.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/example_Coloc_colocResultAll.html -------------------------------------------------------------------------------- /docs/reference/example_Coloc_colocResultsig.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/example_Coloc_colocResultsig.html -------------------------------------------------------------------------------- /docs/reference/example_Coloc_gwasDF.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/example_Coloc_gwasDF.html -------------------------------------------------------------------------------- /docs/reference/example_Coloc_hyprcolocResultAll.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/example_Coloc_hyprcolocResultAll.html -------------------------------------------------------------------------------- /docs/reference/example_Coloc_outGenes.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/example_Coloc_outGenes.html -------------------------------------------------------------------------------- /docs/reference/example_Coloc_sentinelSNP.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/example_Coloc_sentinelSNP.html -------------------------------------------------------------------------------- /docs/reference/example_Coloc_traitsAll.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/example_Coloc_traitsAll.html -------------------------------------------------------------------------------- /docs/reference/extractGeneInfo.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/extractGeneInfo.html -------------------------------------------------------------------------------- /docs/reference/fetchContent.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/fetchContent.html -------------------------------------------------------------------------------- /docs/reference/fetchContentEbi.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/fetchContentEbi.html -------------------------------------------------------------------------------- /docs/reference/gencodeGeneInfoAllGranges.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/gencodeGeneInfoAllGranges.html -------------------------------------------------------------------------------- /docs/reference/gencodeGenetype.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/gencodeGenetype.html -------------------------------------------------------------------------------- /docs/reference/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/index.html -------------------------------------------------------------------------------- /docs/reference/is.wholenumber.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/is.wholenumber.html -------------------------------------------------------------------------------- /docs/reference/retrieveLD.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/retrieveLD.html -------------------------------------------------------------------------------- /docs/reference/retrieveLD_LDmatrix.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/retrieveLD_LDmatrix.html -------------------------------------------------------------------------------- /docs/reference/retrieveLD_LDproxy.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/retrieveLD_LDproxy.html -------------------------------------------------------------------------------- /docs/reference/retrieveLD_LDproxy_old.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/retrieveLD_LDproxy_old.html -------------------------------------------------------------------------------- /docs/reference/sampleNum.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/sampleNum.html -------------------------------------------------------------------------------- /docs/reference/tissueSiteDetailGTExv7.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/tissueSiteDetailGTExv7.html -------------------------------------------------------------------------------- /docs/reference/tissueSiteDetailGTExv8.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/tissueSiteDetailGTExv8.html -------------------------------------------------------------------------------- /docs/reference/xQTL_export.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTL_export.html -------------------------------------------------------------------------------- /docs/reference/xQTLanalyze_TSExp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanalyze_TSExp.html -------------------------------------------------------------------------------- /docs/reference/xQTLanalyze_anno.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanalyze_anno.html -------------------------------------------------------------------------------- /docs/reference/xQTLanalyze_calLambda.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanalyze_calLambda.html -------------------------------------------------------------------------------- /docs/reference/xQTLanalyze_coloc.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanalyze_coloc.html -------------------------------------------------------------------------------- /docs/reference/xQTLanalyze_coloc_diy.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanalyze_coloc_diy.html -------------------------------------------------------------------------------- /docs/reference/xQTLanalyze_enrich.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanalyze_enrich.html -------------------------------------------------------------------------------- /docs/reference/xQTLanalyze_getSentinelSnp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanalyze_getSentinelSnp.html -------------------------------------------------------------------------------- /docs/reference/xQTLanalyze_getTraits.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanalyze_getTraits.html -------------------------------------------------------------------------------- /docs/reference/xQTLanalyze_propensity.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanalyze_propensity.html -------------------------------------------------------------------------------- /docs/reference/xQTLanalyze_qtlSpecificity.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanalyze_qtlSpecificity.html -------------------------------------------------------------------------------- /docs/reference/xQTLanno_calLambda.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanno_calLambda.html -------------------------------------------------------------------------------- /docs/reference/xQTLanno_chippeak.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanno_chippeak.html -------------------------------------------------------------------------------- /docs/reference/xQTLanno_enrich.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanno_enrich.html -------------------------------------------------------------------------------- /docs/reference/xQTLanno_genomic.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLanno_genomic.html -------------------------------------------------------------------------------- /docs/reference/xQTLbiolinks.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLbiolinks.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_egene.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_egene.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_eqtl.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_eqtl.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_eqtlAllAsso.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_eqtlAllAsso.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_eqtlAllAssoPos.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_eqtlAllAssoPos.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_eqtlExp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_eqtlExp.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_eqtlSig.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_eqtlSig.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_exp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_exp.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_geneMedExp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_geneMedExp.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_hqtl.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_hqtl.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_hqtlmeta.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_hqtlmeta.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_ld.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_ld.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_mQTL.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_mQTL.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_mqtlmeta.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_mqtlmeta.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_sc.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_sc.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_scSig.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_scSig.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_sgene.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_sgene.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_sqtlAllAsso.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_sqtlAllAsso.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_sqtlExp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_sqtlExp.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_sqtlSig.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_sqtlSig.html -------------------------------------------------------------------------------- /docs/reference/xQTLdownload_xqtlAllAsso.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLdownload_xqtlAllAsso.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_eqtl.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_eqtl.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_eqtlSig.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_eqtlSig.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_gene.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_gene.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_geneAll.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_geneAll.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_sampleBySampleId.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_sampleBySampleId.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_sampleByTissue.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_sampleByTissue.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_sc.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_sc.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_scInfo.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_scInfo.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_sqtlSig.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_sqtlSig.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_tissue.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_tissue.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_varId.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_varId.html -------------------------------------------------------------------------------- /docs/reference/xQTLquery_varPos.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLquery_varPos.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_PNPlot.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_PNPlot.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_PZPlot.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_PZPlot.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_anno.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_anno.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_coloc.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_coloc.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_enrich.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_enrich.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_eqtl.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_eqtl.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_eqtlExp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_eqtlExp.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_geneCorr.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_geneCorr.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_geneExpTissues.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_geneExpTissues.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_genesExp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_genesExp.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_genoBox.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_genoBox.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_locusCombine.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_locusCombine.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_locusCompare.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_locusCompare.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_locusZoom.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_locusZoom.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_manhattan.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_manhattan.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_qqPlot.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_qqPlot.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_qtlPropensity.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_qtlPropensity.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_qtlSpecificity.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_qtlSpecificity.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_sqtl.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_sqtl.html -------------------------------------------------------------------------------- /docs/reference/xQTLvisual_sqtlExp.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/reference/xQTLvisual_sqtlExp.html -------------------------------------------------------------------------------- /docs/sitemap.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/docs/sitemap.xml -------------------------------------------------------------------------------- /img/Overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/img/Overview.png -------------------------------------------------------------------------------- /inst/extdata/hg19ToHg38.over.chain: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/inst/extdata/hg19ToHg38.over.chain -------------------------------------------------------------------------------- /inst/extdata/sceQTL_study_info.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/inst/extdata/sceQTL_study_info.txt -------------------------------------------------------------------------------- /man/EBIquery_allTerm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/EBIquery_allTerm.Rd -------------------------------------------------------------------------------- /man/apiAdmin_ping.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/apiAdmin_ping.Rd -------------------------------------------------------------------------------- /man/apiEbi_ping.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/apiEbi_ping.Rd -------------------------------------------------------------------------------- /man/dbsnpQueryRange.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/dbsnpQueryRange.Rd -------------------------------------------------------------------------------- /man/ebi_datasets.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/ebi_datasets.Rd -------------------------------------------------------------------------------- /man/ebi_study_tissues.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/ebi_study_tissues.Rd -------------------------------------------------------------------------------- /man/example_Coloc_colocResultAll.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/example_Coloc_colocResultAll.Rd -------------------------------------------------------------------------------- /man/example_Coloc_colocResultsig.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/example_Coloc_colocResultsig.Rd -------------------------------------------------------------------------------- /man/example_Coloc_gwasDF.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/example_Coloc_gwasDF.Rd -------------------------------------------------------------------------------- /man/example_Coloc_hyprcolocResultAll.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/example_Coloc_hyprcolocResultAll.Rd -------------------------------------------------------------------------------- /man/example_Coloc_outGenes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/example_Coloc_outGenes.Rd -------------------------------------------------------------------------------- /man/example_Coloc_sentinelSNP.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/example_Coloc_sentinelSNP.Rd -------------------------------------------------------------------------------- /man/example_Coloc_traitsAll.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/example_Coloc_traitsAll.Rd -------------------------------------------------------------------------------- /man/extractGeneInfo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/extractGeneInfo.Rd -------------------------------------------------------------------------------- /man/fetchContent.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/fetchContent.Rd -------------------------------------------------------------------------------- /man/fetchContentEbi.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/fetchContentEbi.Rd -------------------------------------------------------------------------------- /man/gencodeGeneInfoAllGranges.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/gencodeGeneInfoAllGranges.Rd -------------------------------------------------------------------------------- /man/gencodeGenetype.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/gencodeGenetype.Rd -------------------------------------------------------------------------------- /man/is.wholenumber.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/is.wholenumber.Rd -------------------------------------------------------------------------------- /man/retrieveLD.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/retrieveLD.Rd -------------------------------------------------------------------------------- /man/retrieveLD_LDproxy.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/retrieveLD_LDproxy.Rd -------------------------------------------------------------------------------- /man/sampleNum.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/sampleNum.Rd -------------------------------------------------------------------------------- /man/tissueSiteDetailGTExv7.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/tissueSiteDetailGTExv7.Rd -------------------------------------------------------------------------------- /man/tissueSiteDetailGTExv8.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/tissueSiteDetailGTExv8.Rd -------------------------------------------------------------------------------- /man/xQTL_export.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTL_export.Rd -------------------------------------------------------------------------------- /man/xQTLanalyze_coloc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLanalyze_coloc.Rd -------------------------------------------------------------------------------- /man/xQTLanalyze_coloc_diy.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLanalyze_coloc_diy.Rd -------------------------------------------------------------------------------- /man/xQTLanalyze_getSentinelSnp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLanalyze_getSentinelSnp.Rd -------------------------------------------------------------------------------- /man/xQTLanalyze_getTraits.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLanalyze_getTraits.Rd -------------------------------------------------------------------------------- /man/xQTLanno_calLambda.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLanno_calLambda.Rd -------------------------------------------------------------------------------- /man/xQTLanno_chippeak.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLanno_chippeak.Rd -------------------------------------------------------------------------------- /man/xQTLanno_genomic.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLanno_genomic.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_egene.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_egene.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_eqtlAllAsso.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_eqtlAllAsso.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_eqtlAllAssoPos.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_eqtlAllAssoPos.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_eqtlExp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_eqtlExp.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_exp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_exp.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_geneMedExp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_geneMedExp.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_hqtl.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_hqtl.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_hqtlmeta.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_hqtlmeta.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_mQTL.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_mQTL.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_mqtlmeta.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_mqtlmeta.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_sc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_sc.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_scSig.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_scSig.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_sgene.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_sgene.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_sqtlAllAsso.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_sqtlAllAsso.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_sqtlExp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_sqtlExp.Rd -------------------------------------------------------------------------------- /man/xQTLdownload_xqtlAllAsso.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLdownload_xqtlAllAsso.Rd -------------------------------------------------------------------------------- /man/xQTLquery_eqtl.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_eqtl.Rd -------------------------------------------------------------------------------- /man/xQTLquery_eqtlSig.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_eqtlSig.Rd -------------------------------------------------------------------------------- /man/xQTLquery_gene.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_gene.Rd -------------------------------------------------------------------------------- /man/xQTLquery_geneAll.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_geneAll.Rd -------------------------------------------------------------------------------- /man/xQTLquery_sampleByTissue.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_sampleByTissue.Rd -------------------------------------------------------------------------------- /man/xQTLquery_sc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_sc.Rd -------------------------------------------------------------------------------- /man/xQTLquery_scInfo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_scInfo.Rd -------------------------------------------------------------------------------- /man/xQTLquery_sqtlSig.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_sqtlSig.Rd -------------------------------------------------------------------------------- /man/xQTLquery_tissue.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_tissue.Rd -------------------------------------------------------------------------------- /man/xQTLquery_varId.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_varId.Rd -------------------------------------------------------------------------------- /man/xQTLquery_varPos.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLquery_varPos.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_PZPlot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_PZPlot.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_anno.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_anno.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_coloc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_coloc.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_eqtl.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_eqtl.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_eqtlExp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_eqtlExp.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_geneExpTissues.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_geneExpTissues.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_genesExp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_genesExp.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_genoBox.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_genoBox.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_locusCombine.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_locusCombine.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_locusCompare.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_locusCompare.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_locusZoom.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_locusZoom.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_manhattan.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_manhattan.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_qqPlot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_qqPlot.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_sqtl.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_sqtl.Rd -------------------------------------------------------------------------------- /man/xQTLvisual_sqtlExp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/man/xQTLvisual_sqtlExp.Rd -------------------------------------------------------------------------------- /vignettes/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | *.R 3 | -------------------------------------------------------------------------------- /vignettes/Colocalization_analysis_with_xQTLbiolinks.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/Colocalization_analysis_with_xQTLbiolinks.Rmd -------------------------------------------------------------------------------- /vignettes/Quick_start.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/Quick_start.Rmd -------------------------------------------------------------------------------- /vignettes/images/prostate/anno.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/anno.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_Go.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_Go.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_Go_old.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_Go_old.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_combined.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_combined.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_cor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_cor.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_eQTL_exp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_eQTL_exp.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_eqtlTissues.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_eqtlTissues.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_exp_multissues.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_exp_multissues.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_geneExpInOneTissue.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_geneExpInOneTissue.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_locuscompare.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_locuscompare.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_locuszoom_eqtl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_locuszoom_eqtl.png -------------------------------------------------------------------------------- /vignettes/images/prostate/prostate_locuszoom_gwas.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/prostate_locuszoom_gwas.png -------------------------------------------------------------------------------- /vignettes/images/prostate/qq_plot_all.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/qq_plot_all.png -------------------------------------------------------------------------------- /vignettes/images/prostate/qq_pz_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/qq_pz_plot.png -------------------------------------------------------------------------------- /vignettes/images/prostate/venn_coloc_hyprcoloc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/prostate/venn_coloc_hyprcoloc.png -------------------------------------------------------------------------------- /vignettes/images/quick_start/QQplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/quick_start/QQplot.png -------------------------------------------------------------------------------- /vignettes/images/quick_start/colocalization_framework.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/quick_start/colocalization_framework.png -------------------------------------------------------------------------------- /vignettes/images/quick_start/compare.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/quick_start/compare.png -------------------------------------------------------------------------------- /vignettes/images/quick_start/eQTL_multiple_tissue.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/quick_start/eQTL_multiple_tissue.png -------------------------------------------------------------------------------- /vignettes/images/quick_start/eqtl_legendF.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/quick_start/eqtl_legendF.png -------------------------------------------------------------------------------- /vignettes/images/quick_start/exp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/quick_start/exp.png -------------------------------------------------------------------------------- /vignettes/images/quick_start/gwas_legendF.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/quick_start/gwas_legendF.png -------------------------------------------------------------------------------- /vignettes/images/quick_start/propensity.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/quick_start/propensity.png -------------------------------------------------------------------------------- /vignettes/images/quick_start/xQTLvisual_locusCombine.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/quick_start/xQTLvisual_locusCombine.png -------------------------------------------------------------------------------- /vignettes/images/visualization/eQTLspecificity.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/eQTLspecificity.png -------------------------------------------------------------------------------- /vignettes/images/visualization/geneExpTissues.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/geneExpTissues.png -------------------------------------------------------------------------------- /vignettes/images/visualization/visualization_locusCompare.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/visualization_locusCompare.png -------------------------------------------------------------------------------- /vignettes/images/visualization/visualization_locusZoom.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/visualization_locusZoom.png -------------------------------------------------------------------------------- /vignettes/images/visualization/visualization_locusZoom_eQTL1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/visualization_locusZoom_eQTL1.png -------------------------------------------------------------------------------- /vignettes/images/visualization/visualization_locusZoom_eQTLpos.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/visualization_locusZoom_eQTLpos.png -------------------------------------------------------------------------------- /vignettes/images/visualization/visualization_tissueExp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/visualization_tissueExp.png -------------------------------------------------------------------------------- /vignettes/images/visualization/xQTLvisual_eqtl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/xQTLvisual_eqtl.png -------------------------------------------------------------------------------- /vignettes/images/visualization/xQTLvisual_eqtlExp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/xQTLvisual_eqtlExp.png -------------------------------------------------------------------------------- /vignettes/images/visualization/xQTLvisual_genesExp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/xQTLvisual_genesExp.png -------------------------------------------------------------------------------- /vignettes/images/visualization/xQTLvisual_locusCombine.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/xQTLvisual_locusCombine.png -------------------------------------------------------------------------------- /vignettes/images/visualization/xQTLvisual_sqtlExp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/images/visualization/xQTLvisual_sqtlExp.png -------------------------------------------------------------------------------- /vignettes/query_download.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/query_download.Rmd -------------------------------------------------------------------------------- /vignettes/references.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/references.bib -------------------------------------------------------------------------------- /vignettes/visualization.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lilab-bioinfo/xQTLbiolinks/HEAD/vignettes/visualization.Rmd --------------------------------------------------------------------------------