Software



2015-2017 

 
http://software.buhmhan.com/RE2C
 

RE2C

RE2C is a extended version of the Random Effect model 2 (RE2) implemented in METASOFT

  • Cue. H. Lee., Eleazar. Eskin., Buhm. Han. (in press). "Increasing power of meta-analysis of genome-wide association studies for detecting heterogeneous effects", Bioinformatics
   

BUHMBOX

BUHMBOX is a tool to distinguish pleiotropy and clinical heterogeneitiy.

  • Buhm Han, Jennie G Pouget, Kamil Slowikowski, Eli Stahl, Cue Hyunkyu Lee, Dorothee Diogo, Xinli Hu, Yu Rang Park, Eunji Kim, Peter K Gregersen, Solbritt Rantapaa Dahqvist, Jane Worthington, Steve Eyre, Lars Klareskog, Tom Huizinga, Wei-Min Chen, Suna Onengut-Gumuscu, Stephen S Rich, Major Depressive Disorder Working Group of the PGC, Naomi Wray, Soumya Raychaudhuri “A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases.” Nature Genetics. In Press
 
     http://software.buhmhan.com/FOLD
 

FOLD

FOLD is to obtain a set of summary statistics from each study, where each statistic is calculated using a subset of controls that is homogeneous in terms of their information.

  • Eunji Kim, Buhm Han, "A power-preserving meta-analysis framework for overlapping samples", Under Review



~ 2015

 

SNP2HLA

SNP2HLA imputes HLA genes and amino acids from SNP genotype data.

  • Xiaoming Jia*, Buhm Han*, Suna Onengut-Gumuscu, Wei-Min Chen, Patrick J. Concannon, Stephen S. Rich, Soumya Raychaudhuri, Paul I.W. de Bakker. "Imputing Amino Acid Polymorphisms in Human Leukocyte Antigenes." PLoS One. 8(6):e64683. 2013.
    * : Equal contribution. 

 

METASOFT


METASOFT performs meta-analysis with new random effects model and calculates m-values (posterior probability that effects will exist).

  • Buhm Han, Eleazar Eskin. "Random-Effects Model Aimed at Discovering Associations in Meta-Analysis of Genome-wide Association Studies." The American Journal of Human Genetics. 88(5):586-598, 2011.
  • Buhm Han, Eleazar Eskin. "Interpreting Meta-Analysis of Genome-Wide Association Studies." PLoS Genetics. 8(3):e1002555, 2012.

GraphIBD

GraphIBD performs quick pairwise testing of associations between sharing of IBD segments and disease status.

  • Buhm Han*, Eun Yong Kang*, Soumya Raychaudhuri, Paul I. W. de Bakker, Eleazar Eskin. "Fast Pairwise IBD Association Testing in Genome-wide Association Studies." Bioinformatics. 30(2):206-13. 2014.
    * : Equal contribution.

SLIDE

SLIDE corrects for multiple testing for millions of markers.

  • Buhm Han, Hyun Min Kang, Eleazar Eskin. "Rapid and Accurate Multiple Testing Correction and Power Estimation for Millions of Correlated Markers." PLoS Genetics. 5:4,e1000456, 2009.

LDPAC

LDPAC detects outlier association signal due to genotyping errors.

  • Buhm Han, Brian Hackel, Eleazar Eskin. "Postassociation Cleaning Using Linkage Disequilibrium Information." Genetic Epidemiology. 35(1):1-10, 2011.