M

MIAT software

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.

This project is the source repository of the CRAN package 'SISIR' https://cran.r-project.org/package=SISIR.

This package can perform interval fusion and selection procedures in regression models with functional inputs. Implemented methods include a semiparametric approach based on Sliced Inverse Regression (SIR), as described in doi:10.1007/s11222-018-9806-6 (standard ridge and sparse SIR are also included in the package) and a random forest based approach, as described in doi:10.1002/sam.11705.

Exploration interactive de scenario de simulation du modèle MF1.2-1ha du projet Atcha.

https://mf-12-1-ha.sk8.inrae.fr/ | https://shiny.sk8.inrae.fr/app/atcha-mf-12-1-ha | https://shiny.sk8.inrae.fr/app_direct/atcha-mf-12-1-ha

TP du module 4 de la formation MASTICS https://elearning.formation-permanente.inrae.fr/mod/url/view.php?id=9054

Lien vers l'application : https://mastics-tp-4.sk8.inrae.fr

This project is the source repository of the CRAN package 'RNAseqNet' https://cran.r-project.org/package=RNAseqNet.

This package infers a log-linear Poisson Graphical Model with an auxiliary dataset. Hot-deck multiple imputation method is used to improve the reliability of the inference with an auxiliary dataset DOI:10.1093/bioinformatics/btx819. The package also implements standard log-linear Poisson GM (without missing data) <a href"https://dx.doi.org/10.1109/BIBM.2012.6392619">DOI:10.1109/BIBM.2012.6392619 and the StARS criterion to help with the choice of the regularization parameter.

This project is the source repository of the CRAN package 'treediff' https://cran.r-project.org/package=treediff.

The R package treediff performs Hi-C data differential analysis based on pixel-level differential analysis and a post hoc inference strategy to quantify signal in clusters of pixels. Clusters of pixels are obtained through a connectivity-constrained two-dimensional hierarchical clustering.

Code storage Area of the RECORD Project packages.

This project is the source repository of the CRAN package 'hicream' https://cran.r-project.org/package=hicream.

It performs Hi-C data differential analysis based on pixel-level differential analysis and a post hoc inference strategy to quantify signal in clusters of pixels. Clusters of pixels are obtained through a connectivity-constrained two-dimensional hierarchical clustering.

mixKernel is a multiple kernel framework that allows to integrate multiple datasets of various types into a single analysis. The package is published on CRAN: https://cran.r-project.org/package=mixKernel

This project is the source repository of the CRAN package 'SOMbrero' https://cran.r-project.org/package=SOMbrero.

The stochastic (also called on-line) version of the Self-Organising Map (SOM) algorithm is provided. Different versions of the algorithm are implemented, for numeric and relational data and for contingency tables as described, respectively, in Kohonen (2001) isbn:3-540-67921-9, Olteanu & Villa-Vialaneix (2005) doi:10.1016/j.neucom.2013.11.047 and Cottrell et al (2004) doi:10.1016/j.neunet.2004.07.010. The package also contains many plotting features (to help the user interpret the results), can handle (and impute) missing values and is delivered with a graphical user interface based on 'shiny'.

TP 2 du module 8 de la formation MASTICS https://elearning.formation-permanente.inrae.fr/mod/url/view.php?id=9208

Lien vers l'application : https://mastics-tp-8-2.sk8.inrae.fr

TP 1 du module 8 de la formation MASTICS https://elearning.formation-permanente.inrae.fr/mod/url/view.php?id=9206

Lien vers l'application : https://mastics-tp-8-1.sk8.inrae.fr

TP du module 5 de la formation MASTICS https://elearning.formation-permanente.inrae.fr/mod/quiz/view.php?id=9428

Lien vers l'application : https://mastics-tp-5.sk8.inrae.fr

https://mastics-tp3.sk8.inrae.fr TP du module 3 de la formation MASTICS https://elearning.formation-permanente.inrae.fr/course/view.php?id=419&section=0

erecord web services, web solutions for VLE models of RECORD platform