publications:logiciels
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| ===== Linear models ===== | ===== Linear models ===== | ||
| - | * {{:logiciels:bald_0.1.1.tar.gz|BALD}}: the R package BALD implements/combines functions for Genome-Wide Association Studies including simulation of SNPs data, constrained hierarchical clustering using Linkage Disequilibrium (LD) measures, the Gap statistic to find the optimal number of clusters, and statistical regression models for SNP selection (Univariate, Lasso, Group Lasso, Elastic-Net). | + | * [[logiciels:bald|BALD]] |
| * [[logiciels:jointseg|jointseg]] | * [[logiciels:jointseg|jointseg]] | ||
| * [[logiciels:quadrupen|quadrupen]] | * [[logiciels:quadrupen|quadrupen]] | ||
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| ===== Network Analysis ===== | ===== Network Analysis ===== | ||
| - | * [[http://cran.r-project.org/web/packages/mixer/|Mixer]]\\ | + | * [[http://cran.r-project.org/web/packages/mixer/|Mixer]]: Mixer performs the estimation of Stochastic Blockmodels, a model base clustering method for the nodes of a graph.\\ |
| - | Mixer performs the estimation of Stochastic Blockmodels, a model base clustering method for the nodes of a graph. | + | * [[:logiciels:mixnet|Mixnet]]: A probabilistic mixture model for random graphs, clustering the nodes of a graph. |
| - | + | ||
| - | * [[:logiciels:mixnet|Mixnet]]\\ | + | |
| - | A new probabilistic mixture model for random graphs, clustering the nodes of a graph. | + | |
| - | + | ||
| - | * [[http://example.com|External Link]] | + | |
| * [[logiciels:degraph|DEGraph]] | * [[logiciels:degraph|DEGraph]] | ||
| - | * [[http://cran.r-project.org/src/contrib/Archive/NeMo|NeMo]]\\ | + | * [[http://cran.r-project.org/src/contrib/Archive/NeMo|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.\\ |
| - | R package NeMo performs the detection of over-represented motifs in networks. The underlying null model considered is the Erdös-Rényi mixture for graphs. | + | * [[:logiciels:osbm|OSBM]]: Overlapping Stochastic BlockModels: the R package OSBM clusters the nodes of a graph relying on overlapping groups. |
| - | + | * [[http://cran.r-project.org/src/contrib/Archive/paloma|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. | |
| - | * [[:logiciels:osbm|OSBM]]: Overlapping Stochastic BlockModels\\ | + | |
| - | R package OSBM clusters the nodes of a graph relying on overlapping groups. | + | |
| - | + | ||
| - | * [[http://cran.r-project.org/src/contrib/Archive/paloma|paloma]]\\ | + | |
| - | 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. | + | |
| ===== Network Inference ===== | ===== Network Inference ===== | ||
| - | * [[http://cran.r-project.org/web/packages/G1DBN/index.html|G1DBN]]\\ | + | * [[http://cran.r-project.org/web/packages/G1DBN/index.html|G1DBN]]: R package for reconstruction of gene regulatory networks. G1DBN performs dynamic Bayesian network (DBN) inference using 1st order conditional dependencies. |
| - | //Module R pour la reconstruction de réseaux génétiques : inférence d'un réseau bayésien dynamique à partir d'indépendence d'ordre 1.//\\ | + | * [[:logiciels:simone|Simone]] |
| - | R package for reconstruction of gene regulatory networks. G1DBN performs dynamic Bayesian network (DBN) inference using 1st order conditional dependencies. | + | |
| - | + | ||
| - | * [[:logiciels:simone|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. | + | |
| ===== Sequence Analysis ===== | ===== Sequence Analysis ===== | ||
publications/logiciels.txt · Last modified: 2015/09/07 15:35 by pneuvial
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