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Logiciels / software

mar, 02/17/2009 - 14:06 — schbath

 Sequence analysis

  • pLocalScore, Computing Local Score p-value.
    This program allows to compute asymptotic (Gumble's approximations) and exact p-value for the Local Score of one sequence.
  • R'HOM, Research of HOMogeneous regions in DNA sequences.
    Hidden Markov Models for DNA sequences estimated by likelihood maximisation.
  • R'MES, Finding Exceptional Motifs in Sequences
    A tool to evaluate the statistical significance of motif frequencies in biological sequences.
  • SHOW, Structured HOMogeneities Watcher.
    Hidden Marlov Models for DNA sequences.
  • SIC, Search Inverse Complementary.
    A tool to detect short inverted segments in a biological sequence.
  • SPatt, Statistics for Patterns.
    A complete software package dedicated to the computation of pattern statistics on Markov chains.

 MicroArrays

  • Anapuce,
    Functions for normalisation and differential analysis of microarray data
  • VarMixt,
    Differential analysis of microarray data whose variances are modelled by a mixture model.
  • kerfdr,
    A semi-parametric kernel-based approach to local FDR estimations

 
Association studies

  • exact.allelic.test, A Fast Unbiased and Exact Allelic Test.
    An algorithm dedicated to case-control association studies using bi-allelic markers and allowing to compute fast unbiased exact p-values.
  • LHiSA, Local High-scoring Segments for Association Studies.
    An algorithm dedicated to large-scale association studies which aims to identify segments of genome involved in a disease using local score.

 
 Networks

  • Mix[Net/eR], Erdos-Rényi Mixture for Networks.
    A new probabilistic model for random graphs.

Physical mapping

  • ISLAND
    Program to simulate the progress of an STS physical mapping project.