Softwares and computational codes developed by our group
- iQTL-F2: R code for mapping imprinted quantitative trait loci (iQTL) in F2 experimental cross.
[R Code for genomewide scan]
[R Code for imprinting test].
Reference: Cui, Y.H., Q. Lu, J.M. Cheverud, R.C. Littell and R.L. Wu. (2006) Model for mapping imprinted quantitative trait loci in an inbred F2 design. Genomics 87: 543-551 [PDF]
- R-GC-test: R code for testing genetic conflicts (GC) that increase disease risk in human pregnancy with penalized mixture logistic regression.
[R Code for testing genetic conflicts]
Reference: Li, S.Y., Q. Lu, W. Fu, R. Romero and Y.H. Cui. (2008) A regularized regression approach for dissecting genetic conflicts that increase disease risk in pregnancy. Statistical Applications in Genetics and Molecular Biology [PDF]
- QTL-GPR: Matlab code for QTL mapping with count trait.
[QTL-GPR.zip]
Reference: Cui, Y.H., D.-Y. Kim, and J. Zhu. (2006) On the generalized Poisson regression mixture model for mapping quantitative trait loci with count data. Genetics 174(4): 2159–2172. [PDF]
- QTL-ZIGP: R code for QTL mapping with zero inflated generalized Poisson regression model.
[QTL-ZIGP];
[Sample Data]
Reference: Cui, Y.H. and W.Z. Yang. (2009) Zero-inflated generalized poisson regression mixture model for mapping quantitative trait loci underlying count trait with many zeros. Journal of Theoretical Biology 256: 276-285. [PDF];
- iQTL-VC: R code for iQTL mapping with variance components model in experimental cross. (to be released)
Reference:
Last Modified Sept, 2009