R

R-package

https://metatoul.pages.mia.inra.fr/graphstats

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'.

PatHways lOngitudianal and diffErential aNanlysis in metabolomICS (PHOENICS). Perform differential analysis of metabolic pathways based on longitudinal metabolomics data.

Perform 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.

Landscape Epidemiology and Evolution R package

Docs

CRAN

Shiny app || Shiny Multi app

F3MR is a R package that help to analyze food microbiome omics data based on dedicated and curated metabolic modules based on extensive literature review. It belongs to F3M software suite developed by INRAE Food Microbial Ecology lab

https://umrf.pages.mia.inra.fr/ranomaly/

The SeSAM R package allows fully automatic construction of two successive genetic maps: a first one including an optimized subset of markers ensuring the robustness of orders to a given statistical threshold, and a second one including almost all polymorphic markers. It can handle all common types of biparental mapping populations, including progenies obtained from crossing heterozygous parents. In addition to the automatic procedure, SeSAM includes many functions for interactive mapping, file formats conversions, and generates many graphs useful to assess the quality of data and maps.

R package to run MuSICA

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

shinySbm is a package containing a shiny application. This application is build for network analysis based on the sbm package made by Chiquet J, Donnet S and Barbillon P (2023) CRAN. It allow to apply and explore the outputs of a Stochastic Block Model. It is useful if you want to analyse your data (could be adjacency matrix or edges list) without R language knowledge or to learn the basic lines of the sbm package.

ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity. Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology.

Produce an epidemiological risk map by weighting multiple risk factors. https://umr-astre.pages.mia.inra.fr/mapMCDA/

Match toponyms by similarity

Analyse mark-release-recapture data from Sterile Insect Technique (SIT) field experiments. https://umr-astre.pages.mia.inra.fr/sit

The aim of the eggbiomechanic package is to allow a rapid and reproducible analysis of the biomechanical parameters of the chicken egg.

The aim of this package is to provide a full genomic features annotation from genomic coordinates, without use an annotation priority.

R package for modelling arthropod development rates (mean and variance) as a function of temperature in nimble. Adapted from the PhD work of Soledad Castano (http://www.theses.fr/223623849).