Logiciels

HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular .tsv files, Cooler .cool or .mcool files, Juicer .hic files or HiC-Pro .matrix and .bed files.

SISIR is an R package that implements interval fusion and selection procedures for regression with functional inputs. Models include a semiparametric approach based on Sliced Inverse Regression (SIR) and a random forest based approach. A typical use case of SISIR is the search for time intervals in weather time series, during which the value of the weather impacts the most the yield of fields.

metagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.

GMtoolbox propose un ensemble de fonctions permettant de représenter un modèle graphique sous forme de graphe de facteurs (factor graph) et d’inférer des marginales possiblement avec observations. La toolbox est actuellement disponible dans l’environnement MATLAB.

D-GENIES is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library. D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.

GMDPtoolbox propose un ensemble de fonctions relatives à la résolution de Processus Décisionnels de Markov sur Graphe (Graph-based Markov Decision Processes en anglais). La toolbox est actuellement disponible dans l’environnement MATLAB.

GPGame est un paquet dédié à la recherche d’équilibre de jeux (Nash, etc.) par optimisation bayésienne.

Kernel-based methods are powerful methods for integrating heterogeneous types of data. mixKernel provides methods to combine multiple kernels for unsupervised exploratory analysis or to select features in a kernel for unsupervised analysis or kernel-output prediction. For the multiple kernel problem, different solutions have been implemented to obtain a consensus kernel or a kernel that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a nonlinear space and from the multiple source point of view. Functions to assess and display important variables using permutations are also provided in the package.

GADAG est un paquet dédié à l’apprentissage de graphes acycliques dirigés (DAG) creux.

In sRNAseq data sets, only a very small fraction of reads can be assigned to a known functionnal family resulting in a lot of sRNAseq data orphan of functional annotation. The bias introduced by errors, the editing of some sequences but also the lack of similarities in existing ncRNA databases make challenging their structural and functional annotation. sRNAseq data analysis tools such as miRDeep, miRanalyzer and others focus on microRNAs annotation and prediction, neglecting other types of RNAs. Recently, web tools such as DARIO, Ncpro enlarged functional annotation. sRNAbrowse is a software under development which aims at profiling, annotating and exploring as many sRNAseq data as possible, considering different ncRNA families and differential expression in multiple conditions and/or tissues.

SOMbrero is an R package that implements stochastic self-organizing maps (SOM) variants for numeric and non numeric datasets.

GPareto est un paquet dédié à l’optimisation multi-objectifs à l’aide de processus gaussiens.

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quiet diverse. RNAbrowse is an user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data.

Description: jvenn is a plug-in for the jQuery Javascript library. It is a flexible tool, based upon the venny tool first developed by J.C Oliveros (Oliveros, J.C (2007) VENNY, An integrative tool for comparing lists with Venn Diagrams). Key features: hanldes up to 6 classes venn diagram, allows to display Edwards-Venn diagram, is easily integrable within your own web site, allows to provide the data from 3 different ways (lists/intersection counts/count lists), control the click callback function, provides statistic charts based on input data, search for elements, exports the venn diagram to PNG and SVG, exports lists to CSV.

Warning: Please note that we are not adding any new features to this software.

DiceOptim propose un ensemble de fonctions pour l’optimisation bayésienne dans les cas simples, bruités ou avec contraintes.