Software and Resources

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.

Oxford Brain Imaging Genetics (BIG) server – a browser for 3,144 GWAS of brain imaging derived phenotypes in the UK Biobank, based on Elliott, L. et al (2017)

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

PHASING SERVER  – a service for accurately phasing sequenced samples using large haplotype reference panels, such as the Haplotype Reference Consortium dataset.

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

GTOOL – a program for (a) generating subsets of genotype data, and (b) converting genotype data between the PED file format and the FILE FORMAT used by SNPTEST and IMPUTE.

FastICA – R package that implements the FastICA algorithm

AnalyzeFMRI –  R package for visualisation and analysis of FMRI data

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