http://www.math-evry.cnrs.fr/ 2026-08-13T13:29:49+02:00 http://www.math-evry.cnrs.fr/ http://www.math-evry.cnrs.fr/lib/tpl/lamme/images/favicon.ico text/html 2020-02-17T16:23:45+02:00 http://www.math-evry.cnrs.fr/logiciels/bald?rev=1581953025&do=diff BALD software home page Overview * Title: Blockwise Approach using Linkage Disequilibrium information * Language: R * Description: Functions for the 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). text/html 2015-09-07T15:48:46+02:00 http://www.math-evry.cnrs.fr/logiciels/degraph?rev=1441633726&do=diff DEGraph software home page Overview * Title: Two-sample tests on a graph * Language: R * Description: DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of … text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/drimm?rev=1417186312&do=diff DRIMM - Welcome DRIMM (Drifting Markov Models) General Description DRIMM is a software dedicated to the estimation of Drifting Markov Models (see [1] and [2]). See a more detailed description at this page. [1] Vergne, N. Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences. Statistical Applications in Genetics Molecular Biology 2008, vol 7, issue 1. text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/fueatest?rev=1417186312&do=diff A Fast Unbiased and Exact Allelic Test 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 co… text/html 2015-09-07T16:12:26+02:00 http://www.math-evry.cnrs.fr/logiciels/jointseg?rev=1441635146&do=diff jointseg software home page Overview * Title: Joint segmentation of multivariate (copy number) signals * Description: This package implements functions to quickly segment multivariate signals into piecewise constant profiles and a framework to generate realistic copy-number profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies. text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/kerfdr?rev=1417186312&do=diff kerfdr The use in Biology of current high-throughput genetic and post-genomic data leads to the simultaneous evaluation of a huge number of statistical hypothesis and at the same time, to the multiple-testing problem. As an alternative to the too conservative Family-Wise Error-Rate (FWER), the text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/lhisa?rev=1417186312&do=diff Local High-scoring Segments for Association 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. Our algorithm is fast and available under different versions: text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/mixnet?rev=1417186312&do=diff MixNet software homepage This work results from a collaboration in the Statistics for Systems Biology group between * the Agroparistech Statistics and Genome group, * the CNRS/UEVE/INRA Statistics and Genome laboratory, * the Biometry and Evolutionnary Biology laboratory. Context We present a software package based on a new probabilistic model for random graphs called MixNet (Erdös-Renyi Mixture for Networks). This model is based on the hypothesis that real networks are made … text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/ms4?rev=1417186312&do=diff MS4: Multi Scale Selector of Sequence Signatures Download the latest version [here]. This implementation t_MS4 is a beta release of the MS4 algorithm. t_MS4 uses previous development : NLD-decoding to find NLD classes (C part of the code, included) and text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/osbm?rev=1417186312&do=diff Overlapping Stochastic BlockModel Download the R package [here]. The package will soon be available on the CRAN. A model based clustering method for clustering the nodes of a graph according to a similar connectivity behaviour. The model allows the vertices to belong to multiple clusters, and, to some extent, generalizes the well known Stochastic BlockModel. text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/panow?rev=1417186312&do=diff PANOW - Welcome PANOW (Poisson Approximation for the Numbers of Occurrences of Words) General description PANOW is a software dedicated to the search of rare words in biological sequences (over- or under-represented words in DNA or protein sequences). Using recent results on occurrence times of a string of symbols in a stochastic process with mixing properties (such as Markov chains), it computes point by point error between the law of the number of occurrences of a word and the Poisson appro… text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/quadrupen?rev=1417186312&do=diff Quadrupen software home page Context This package fits classical sparse regression models with efficient active set algorithms by solving quadratic problems. Also provides a few methods for model selection purpose. Download stable version on CRAN now. Also check the R-forge dev page for the text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/scoop?rev=1417186312&do=diff Scoop software home page Context The scoop (Sparse cooperative regression) R package fits coop-Lasso, group-Lasso and Lasso solution paths for linear regression and logistic regression. The cooperative-Lasso (in short coop-Lasso) may be viewed as a modification of the group-Lasso penalty that promotes sign coherence and that allows zeros within groups. text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/ships?rev=1417186312&do=diff SHIPS homepage Overview 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 text/html 2014-11-28T15:51:52+02:00 http://www.math-evry.cnrs.fr/logiciels/simone?rev=1417186312&do=diff SIMONe software home page Context SIMoNe (Statistical Inference for MOdular NEtworks) is an R package which implements the inference of co-expression networks based on partial correlation coefficients from either steady-state or time-course transcriptomic data. Note that with both type of data this package can deal with samples collected in different experimental conditions and therefore not identically distributed. In this particular case, multiple but related graphs are inferred on one simo… text/html 2015-09-07T16:12:52+02:00 http://www.math-evry.cnrs.fr/logiciels/tmle.npvi?rev=1441635172&do=diff tmle.npvi software home page Overview * Title: Targeted Learning of a Non-Parametric Variable Importance Measure of a Continuous Exposure * Language: R * Description: Targeted minimum loss estimation (TMLE) of a non-parametric variable importance measure of a continuous exposure 'X' on an outcome 'Y', taking baseline covariates 'W' into account.