PrediXcan specifications

Information


Unique identifier OMICS_08952
Name PrediXcan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Python, R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Hae Kyung Im <>

Publication for PrediXcan

PrediXcan in publications

 (15)
PMCID: 5940825
PMID: 29739930
DOI: 10.1038/s41467-018-03621-1

[…] functional consequences of genetic variation at the transcript level., to integrate knowledge generated from these large-scale transcriptome studies and shed light on disease biology, we developed predixcan, a gene-level association approach that tests the mediating effects of gene expression levels on phenotypes. predixcan is implemented on gwas or sequencing studies (i.e., studies […]

PMCID: 5863845
PMID: 29566699
DOI: 10.1186/s12931-018-0744-9

[…] we tested significant genes from dgn-blood and gtex-lung in two independent reference transcriptome databases, gtex for whole blood (gtex-blood) and the lung-eqtl consortium for lung tissue using s-predixcan and twas/fusion (additional file : supplementary methods). we considered an expression result to be validated if the direction of effect was consistent and the bonferroni-corrected p-value […]

PMCID: 5872085
PMID: 29495422
DOI: 10.3390/jpm8010011

[…] fastbat method, which derives the association p-value for a set of snps from an approximated distribution of the sum of chi-squared statistics []. second, we performed an eqtl-based analysis using predixcan []. predixcan predicts the genetically determined transcriptome using an eqtl database specific for cardiac ventricle tissue, and correlates the predicted gene expression with phenotypes. […]

PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] cell types . here, we will simply match gwas snps and eqtls according to their genomic locations, which is a rather crude way to integrate these two types of data. more robust alternatives such as predixcan , twas and smr exist and should be adopted if possible. one downside of these methods is that they require subject-level or complete summary data, making them less practical […]

PMCID: 5814451
PMID: 29449654
DOI: 10.1038/s41598-018-20435-9

[…] the approaches implemented in metaxcan fastbat, and eugene. we used the gwas results from oag as well as combined oag and its endophenotypes for the gene-based tests. metaxcan is an extension of predixcan, a gene-based approach that uses gwas summary results to impute the genetic component of gene expression in different tissues (thus eliminating the need to directly measure gene expression […]


To access a full list of publications, you will need to upgrade to our premium service.

PrediXcan institution(s)
Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL; Division of Genetic Medicine, Vanderbilt University, Nashville, TN; Department of Biomedical Informatics, Vanderbilt University, Nashville, TN; Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL; Department of Human Genetics, University of Chicago, Chicago, IL; Department of Statistics, University of Chicago, Chicago, IL

PrediXcan reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PrediXcan