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Software
- Bach: Bausch's algorithm for chi-squared weighted sum
- This software computes tail probability of a mixture of chi-squared random variables. We (I mean former graduate stuent Quan Zhou) implmented Bausch's algorithm using GNU GMP library so that a tail probability (or p-value) can be evaluated to an arbitrary precision. It is the companion software for a manuscript written by Zhou and Guan Null distribution of Bayes factors.
- Download and Documentation
- BIMBAM: Baysian Imputation Based Association Mapping
- The software performs genotype imputation and statistical tests for disease association, including single SNP tests and regional multi-SNP tests. This is the companion software for the paper Practical issues in imputation.
- Download and Documentation
- ELAI: Efficient Local Ancestry Inference
- The software performs local ancestry inference for admixed individuals. It is the companion software for the paper Local ancestry inference.
- Download and Documentation on github
- New multi-threading ELAI
- hapQTL: haplotype Quantitative Loci
- This software performs association testing between local haplotypes and phenotypes at each core marker. It is the companion software for the paper Haplotype QTL.
- Download and Documentation
- IDUL: Iterative dispersion udpate to fit linear mixed model
- IDUL is designed for multi-omics analysis where each SNPs are tested for association with many phenotypes. IDUL has both theoretical and practical advantages over the Newton-Raphson method. Manuscript will be available shortly.
- IDUL Linux Excutable (Version 0.83)
- Source code and Mannual on github
- Kindred: Infer kinship and inbreeding coefficients
- Kindred is designed to infer kinship phi between a pair of samples accounting for inbreeding of the samples. This is done through modelling nine latent Jacquard IBD states. If the pair is one and itself, the kinship is phi = (1+F)/2 where F denotes inbreeding coefficient. Manuscript will be available shortly.
- Kindred Linux Excutable (tarred)
- Kindred Mac Executable (tarred)
- Source code and Mannual on github
- Nubeam-dedup de-duplicate sequencing reads without mapping
- Nubeam-dedup represents nucleotides by matrices, transforms reads into products of matrices, and based on which assigns a unique number to a read. Thus, duplicate reads can be efficiently removed by using a collisionless hash function. This is the companion software for the paper Nubeam-dedup Bioinforamtics.
- Download and Documentation on github
- piMASS: posterior inference via Model Averaging and Subset Selection
- The software performs genome-wide joint analysis of all SNPs in association with a phenotype. We use Markov chain Monte Carlo to perform subset selection and model averaging. This is the companion software for the paper Bayesian variable selection regression.
- Download and Documentation
- WinSSS: Windows-based Stochastic Spatial Simulator
- This is a Windows-based software. It implements many classical models in interacting particle systems, for example, the multiple contact process, the Greenberg Hastings process, and the generalized Rock-Scissor-Paper dynamic. The real time animations are rendered by openGL.
- Download and Documentation
- Source code for WinSSS