0. Belief Propagation- This project seeks to implement generic belief propagation in order to do efficient on graphical models. It will also allow for optimizations using parallel computing and efficient memory management.
2. ddepn- DDEPN (Dynamic Deterministic Effects Propagation Networks): Infer signalling networks for high-throughput genomic or proteomic timecourse data, generated after external perturbation like activation or inhibition of network nodes.
Development Status : 5 - Production/Stable [Filter]
3. Genome-wide analysis using MOSS- Performs genome-wide analysis of dense SNP array data using the mode oriented stochastic search (MOSS) algorithm in a case-control design. Includes preprocessing of the data from Plink format to the format required by the MOSS algorithm.
4. Test for point containment in polyhedron- This project provides a function to test whether a point is contained within a closed three-dimensional polyhedron, defined by a triangular mesh. A two-dimensional version for polygons is also provided.
5. Statistical methods for visual fields- a collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualisation, statistical analysis, and clinical interpretation of visual field loss and its change over time
7. Statistical analysis of DNA mixtures- Statistical analysis of mixed traces of DNA with artefacts. Features include parameter-fitting, visual diagnostics, evaluation of the likelihood, and genotype prediction. Full functionality requires a licenced copy of Hugin (www.hugin.com).
8. geneNetBP- The geneNetBP package implements methods to predict, quantify and visualize system-wide changes in beliefs after absorbing evidence in genotype-phenotype networks inferred from eQTL data.