BALD, DEGraph, DRIMM, G1DBN, jointseg, Mixer, Mixnet, MS4, NeMo, OSBM, paloma, Panow, quadrupen R'HOM, scoop, Seq++, SHOW, Simone, tmle.npvi

• BALD
• jointseg
• quadrupen
• scoop
• tmle.npvi

• Mixer: Mixer performs the estimation of Stochastic Blockmodels, a model base clustering method for the nodes of a graph.
  
• Mixnet: A probabilistic mixture model for random graphs, clustering the nodes of a graph.
• DEGraph
• NeMo: the R package NeMo performs the detection of over-represented motifs in networks. The underlying null model considered is the Erdös-Rényi mixture for graphs.
  
• OSBM: Overlapping Stochastic BlockModels: the R package OSBM clusters the nodes of a graph relying on overlapping groups.
• paloma: the R package paloma performs the detection of locally over-represented motifs in networks. The underlying null model considered is the Erdös-Rényi mixture for graphs. The difference with other motif detection tools is that the statistic considered is not the overall count of patterns of size n but the maximum number of such patterns sharing a subpattern of size n-1.

• G1DBN
  

Module R pour la reconstruction de réseaux génétiques : inférence d'un réseau bayésien dynamique à partir d'indépendence d'ordre 1.
R package for reconstruction of gene regulatory networks. G1DBN performs dynamic Bayesian network (DBN) inference using 1st order conditional dependencies.

• Simone
  

SIMoNe (Statistical Inference for MOdular NEtworks) is a R package which enables inference of gene-regulatory networks based on partial correlation coefficients from microarray experiments. Modelling gene expression data with a Gaussian Graphical Model, the algorithm estimates nonzero entries of the concentration matrix, in a sparse and possibly high-dimensional setting. Its originality lies in the fact that it searches for a latent modular structure to drive the inference procedure through adaptive penalization of the concentration matrix.

• DRIMM
  

DRIMM is a software dedicated to the estimation of Drifting Markov Models (DMM). DRIMM provides four programs:

1. DRIMM: Estimation of DMM by different methods.
2. PVALUEdmm: Compute the p-value of a word under a DMM. This program needs a configuration file generated by DRIMM and a markov file generated by Spatt.
3. PROBAword : Compute, at each position in the sequence, the probability that a word appears. This program needs a configuration file generated by DRIMM.
4. PROBAlength : Compute, at each position, the probability of appearance of the word of size length who appears in this position. This program needs a configuration file generated by DRIMM.

• MS4

« Multi-Scale Selector of Sequence Signatures » est une méthode de classification de séquences biologiques sans alignement.
Multi-Scale Selector of Sequence Signatures is an alignment-free method for classification of biological sequences.

• R'HOM
  

Research of HOMogeneous regions in DNA sequences.
R'HOM (Recherche de régions HOMogènes) est un programme pour la segmentation de séquences d'ADN en régions de composition homogènes par chaînes de Markov cachées. L'utilisateur choisi le nombre de type de composition différentes et la longueur des mots à prendre en compte. Les paramètres sont ensuite estimés par maximum de vraisemblance (algorithme EM) et la séquence est finalement segmentée avec l'algorithme forward backward. R'HOM a été initialement développé pendant la thèse de doctorat de Florence Muri et a été ensuite en grande partie ré-implémenté.

• Seq++
  

Bibliothèque de classes pour la modélisation et l'analyse de séquences biologiques à l'aide de chaînes de Markov.
The seq++ package offers: a C++ object-oriented Library for developers and a reference set of programs for biologists working on sequences and statistics.

• SHOW
  

SHOW (Structured HOMgeneity Watcher) permet une utilisation souple des modèles de chaînes de Markov cachées. L'utilisateur peut construire son propre modèle dont les paramètres peuvent ensuite être estimés par maximum de vraisemblance avec l'algorithme EM. Le modèle peut alors servir à faire des prédictions avec l'algorithme forward-backward (posterior decoding) ou avec l'algorithme de Viterbi. Il peut aussi servir à simuler des séquences. SHOW implémente aussi un détecteur de gènes bactériens. L'utilisateur n'a alors pas à se soucier du modèle ni des paramètres. SHOW a déjà servi a annoter des genomes complets publiés.

• FUEATEST
  

The Fast Unbiased and Exact Allelic Test is dedicated to case-control association studies using bi-allelic markers. Since the allelic test as it is classically performed via Chi-square or Fischer-exact tests, introduce a bias that results in putative false predictions, we developped this test as an efficient alternative. It computes an unbiased and exact p-value. Fast (due to a clever implementation) and availbable under different versions, this test is convenient for any use.

• kerfdr
  

A semi-parametric kernel-based approach to local FDR estimations.

• LHiSA
  

LHiSA is an algorithm dedicated to large-scale association studies which aims to identify segments of genome involved in a disease. It is based on Local Score statistic and an automatic selection of the significant segments.

• SHIPS
  

SHIPS (Spectral Hierarchical Clustering for the Inference of Population Structure) is a non-parametric clustering algorithm that clusters individuals from a population into genetically homogeneous sub-populations from genotype data. After computing a pairwise distance matrix, the algorithm progressively divides the original population in two sub-populations by the use of a spectral clustering algorithm. The process is then iterated in each of the two sub-populations and so on. This leads to the construction of a binary tree, where each node represents a group of individuals. To determine the final clusters a tree pruning procedure and an estimation of the optimal number of clusters, that is a gap statistic, are applied. In such an approach both the final clustering of the individuals and the number of clusters are estimated by the method.

• Panow
  

PANOW (Poisson Approximation for the Numbers of Occurrences of Words) est un logiciel pour la recherche de mots rares dans des séquences biologiques.
Searching for words with rare occurrences in biological sequences.

• pLocalScore
  

Computation of maximal local score of a sequence.

• SIC
  

SIC : Scan Inverse Complementary.
Logiciel pour la recherche de segments inversés dans les séquences biologiques.
Software for the search of short inverted segments in biological sequences.

• SPatt
  

Logiciel d'analyse statistique des motifs dans les séquences biologiques.
Software for statistical analysis of sequence motifs.