This page contains links to software packages that were developed by our group.
If you have questions use the OXSTATGEN MAIL LIST, and post a question there.
Please read the LICENCE information before using these programs.
SDA4D – a program for sparse 4D tensor decomposition
LEMMA is a whole genome wide regression method for flexible modeling of gene-environment interactions in large datasets such as the UK Biobank.
GPLEMMA is a non-linear randomized Haseman-Elston regression for estimation of gene-environment heritability for flexible modeling of gene-environment interactions in large datasets such as the UK Biobank.
IMPUTE 5 – a program for pre-phasing based genotype imputation based on the PBWT.
BGENIE – a program for multiple trait GWAS focussed on the BGEN format files used to store the UK Biobank genetic data on ~500,000 individuals.
SDA – a program for sparse Bayesian matrix and tensor decomposition
IMPUTE 4 – a program for pre-phasing based genotype imputation.
IMPUTE 2 – a program for genotype imputation and phasing in genome-wide association studies and fine-mapping studies based on a dense set of marker data (such as 1000 Genomes Project haplotypes)
SHAPEIT 2 – a program for accurate and efficient phasing of genetic datasets
SHAPEIT 3 – a program for accurate and efficient phasing of very large genetic datasets
SNPTEST – a program for Frequentist and Bayesian tests of SNP association with binary (case-control) and quantitative phenotypes that takes genotype uncertainty into account.
SBAT – a program for Sparse Bayesian Association Testing that can fit full and sparse multi-trait linear mixed models.
PHENIX – an R package for multiple trait imputation in genetic studies.
DUOHMM – a program that works together with SHAPEIT to produce accurate inference of haplotypes in pedigrees, estimate recombination events and detect genotyping errors.
MVNCALL – a program for genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold.
HAPGEN – a program to simulate case control datasets at linked SNP markers conditional upon a set of known haplotypes.
GWAPOWER – an R package for assessing the power of genome-wide association studies using commercially available genotyping chips. The package encapsulates extensive simulation results generated by our program HAPGEN and described fully in the paper
MULTIMIX – a program for admixture deconvolution using multiple (i.e. > 2) phased or unphased ancestral panels.
META – a program to carryout meta-analysis of genetic studies.
GENECLUSTER – a program for location and detection of unobserved causal loci in fine-mapping experiments and genome-wide association studies.
CHIAMANTE – a joint genotype calling algorithm for array and sequence data. This method can be used to call genotype from just array data.
CHIAMO – a genotype calling algorithm for multi-cohort studies.
QCTOOL – a program for carrying out SNP and sample quality control (QC) for genome-wide association studies
FastICA – R package that implements the FastICA algorithm
AnalyzeFMRI – R package for visualisation and analysis of FMRI data