R

R-package

Estimate the spread-rate of epidemics https://umr-astre.pages.mia.inra.fr/spreadrate/

The aim of this package is to allow a rapid and reproducible enhanced analysis of the mass spectrometry results provided by ScaffoldProteome software.

Requirements and design of a R package for analysing data from Mark-Capture-Recapture experiments for the effective management of invasive Aedes mosquitoes.

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).

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

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

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

Match toponyms by similarity

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

Networks/graphs with geo-localised nodes https://umr-astre.pages.mia.inra.fr/geonetwork/

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.

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

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

https://etienne.rifa.pages.mia.inra.fr/graphstats

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.

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.

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