0. 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.
1. 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.
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. 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
4. 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.
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).
9. 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.