Software

Please see my github page also.


  • PrediXcan
    1. A gene-based association method for mapping traits using reference transcriptome data. Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC; GTEx Consortium, Nicolae DL, Cox NJ, Im HK. Nature Genetics. 2015 Aug 10. doi: 10.1038/ng.3367. [Epub ahead of print] PMID: 26258848.
  • SCAN: SNP and CNV annotation database (GEO: GSE9703, GSE39672)
    1. SCAN: SNP and copy number annotation. Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, et al. Bioinformatics. 2010 Jan 15;26(2):259-62. PMID: 19933162.
    2. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, et al. PLoS Genetics. 2010 Apr 1;6(4):e1000888. PMID: 20369019.
    3. SCAN database: facilitating integrative analyses of cytosine modification and expression QTL. Zhang W*, Gamazon ER*, Zhang X*, Konkashbaev A, Liu C, Szilágyi KL, Dolan ME, Cox NJ. Database (Oxford). 2015 Mar 27;2015. pii: bav025. doi: 10.1093/database/bav025. Print 2015. PMID: 25818895. *Contributed equally.
  • PACdb: a pharmacogenetics-cell line database
    1. PACdb: a database for cell-based pharmacogenomics. Gamazon ER, Duan S, Zhang W, Huang RS, Kistner EO, et al. Pharmacogenet Genomics. 2010 Apr;20(4):269-73. PMID: 20216476.
    2. Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci. Gamazon ER, Huang RS, Cox NJ, Dolan ME. Proceedings of the National Academy of Sciences. 2010 May 18;107(20):9287-92. Epub 2010 May 4. PMID: 20442332.
  • Local_ancestry
    1. Zhong Y, Perera M, Gamazon ER. On using local ancestry to characterize the genetic architecture of human phenotypes: Genetic regulation of gene expression in a multiethnic or admixed populations as a model. In revision.
  • ExprTargetDB: An expression-corroborated catalogue of human microRNA targets (GEO: GSE34406)
    1. Exprtarget: an integrative approach to predicting human microRNA targets. Gamazon ER, Im HK, Duan S, Lussier YA, Cox NJ, et al. PLoS One. 2010 Oct 21;5(10):e13534. PMID: 20975837.
  • OmicKriging R package
    1. Poly-Omic Prediction of Complex Traits: OmicKriging. Wheeler HE, Aquino-Michaels K, Gamazon ER, Trubetskoy VV, Dolan ME, Huang RS, Cox NJ and Im HK. (2014), Poly-Omic Prediction of Complex Traits: OmicKriging. Genetic Epidemiology. doi: 10.1002/gepi.21808.
  • eFDR
    1. Integrative Genomics: Quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. Gamazon ER, Huang RS, Dolan ME, Cox NJ, Im HK. Frontiers in Statistical Genetics and Methodology. 3:202. doi: 10.3389/fgene.2012.00202. PMID: 23755062.
  • GxTheta
    1. An ancestry based approach for detecting interactions. Park DS, Eskin I, Kang EY, Gamazon ER, Eng C, Gignoux CR, Galanter JM, Burchard E, et al.
  • MixRF
    1. Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx. Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LS. American Journal of Human Genetics. 2016 Mar 29. pii: S0002-9297(16)00071-9. doi: 10.1016/j.ajhg.2016.02.020. [Epub ahead of print] PMID: 27040689.