2026-10-13T15:08:32Z https://www.scidb.cn/oai

10.57760/sciencedb.08092 2023-10-30T11:06:03Z

2023-10-30 PigGTEx_v0 - Analysis Pipeline doi:10.57760/sciencedb.08092 en This repository contains analysis pipelines used by the pilot phase (V0) of PigGTEx project, including:Whole-genome sequence alignment, SNP calling, and quality controlRNA-seq alignment, quantification, SNP calling, genotype imputation, and quality controlTissue-specific gene expression and co-expression analysisBioinformatics analysis of WGBS dataSingle-cell RNA-Seq analysisBreed prediction for RNA-Seq samplesCis-heritability estimation for gene expressionMolecular QTL (molQTL) mapping, meta-analysis, effect size measurement, and evolutionary conservationAllele-specific expression (ASE) analysisFunctional annotation (snpEff and chromatin state) of molQTLInterpreting GWAS loci with molQTL: enrichment, expression-mediated heritability, transcriptome-wide association study, Mendelian Randomization, and co-localizationComparative analysis between pig and human FarmGTEx; GWAS; Regulatory variants; PigGTEx; Integrative genomics The PigGTEx Consortium PUBLIC https://api.github.com/licenses/cc0-1.0 dataset http://www.doi.org/10.21203/rs.3.rs-2261680/v1 Science Data Bank