R packages
- GeneGeneInteR: The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results.
- SpatialClustering: The aim of this package is to propose a method for detecting clusters of points in bi-dimensional space. Our method allows to account for a covariate in the clustering. The package proposes a graphical visualization of the clusters.
- Reference: A. Bar-Hen, M. Emily and N. Picard. (2015) Spatial Cluster Detection Using Nearest Neighbour Distance, Spatial Statistics, Vol. 14, pages 400-411.
- [Web] on Github.
- SMILE: The aim of this package is to propose an implementation of the SMILE statistical method. Such a method aims at detecting subpopulation(s) (breed for example) under selection. Based on the haplotype data in a given genomic region, the method computes the d2s dissimilarity and performs a hierarchical clustering to extract the subpopulation under selection.
- Reference: M. Emily , C. Hitte and A. Mom (2016) SMILE: a novel Dissimilarity-based Procedure for Detecting Sparse-Specific Profiles in Sparse Contingency Tables, Computational Statistics and Data Analysis, Vol. 99, pages 171-188.
- [Web] on Github.
- EpiTag: The aim of this package is to propose a method for selecting TagSNPs to optimize power for detecting epistasis.
- Reference: M Emily and C. Friguet (2018) A survey of statistical methods for gene-gene interaction in case-control genome-wide association studies, Journal de la Société Française de Statistique, Vol. 159, No. 2, pages 84-110.
- [Web] on Github.
- IndOR: The aim of this package is to propose an implementation of the IndOR statistical method. Such a method aims at detecting SNPxSNP interaction by testing the independence between Odds-Ratio.
- Reference: M. Emily (2012) IndOR: A new statistical procedure to test for SNP-SNP epistasis in Genome-Wide Association Studies, Statistics In Medicine, Vol. 31, No. 21, pages 2359-2373.
- [Web] on Github.
- Metamyl is a meta-predictor of the aggregation of proteins or peptides in amyloid fibrils. In more details, Metamyl aims at combining existing methods into a meta-predictor for hot spots prediction, called MetAmyl for METapredictor for AMYLoid proteins. MetAmyl is based on a logistic regression model that aims at weighting predictions from a set of popular algorithms, statistically selected as being the most informative and complementary predictors.
- Reference: M. Emily, A. Talvas and C. Delamarche. (2013) MetAmyl: a METa-predictor for AMYLoid proteins, PLoS One, 8(11): e79722.
- [Web] on Github.
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