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/

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.

This repository moved to https://gitlab.cirad.fr/astre/geonetwork

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

R package to compute Sentinel-2 Nadir BRDF Adjusted Reflectance

Documentation

https://explore-metabar.sk8.inrae.fr/

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

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'.

Landscape Epidemiology and Evolution R package

Docs

CRAN

Shiny app || Shiny Multi app