SOMbrero

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

Role in the project: Maintainer and author

 install.packages("SOMbrero") 

 sombreroWUI() 

SISIR

SISIR is an R package that implements the sparse interval sliced inverse regression. It also provides an implementation of standard ridge and sparse SIR for high dimensional data

Role in the project: Maintainer and author

 install.packages("SISIR") 

RNAseqNet

RNAseqNet is an R package that implements network inference with log-linear Poisson Graphical Model. Hot-deck multiple imputation method can be used to improve the reliability of the inference with an auxiliary dataset.

Role in the project: Maintainer and author

 install.packages("RNAseqNet") 

mixKernel

mixKernel is an R package that provides methods to combine kernels for unsupervised exploratory analysis. Different solutions are implemented to compute a meta-kernel, in a consensus way or in a way that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a non linear space and from the multiple source point of view. Functions to assess and display important variables are also provided in the package.

Role in the project: Author (Maintainer is Jérôme Mariette)

 install.packages("mixKernel") 

ASICS

ASICS is an R package that quantifies metabolites concentration in a complex spectrum using a set of pure metabolite spectra. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty.

Role in the project: Author (Maintainer is Gaëlle Lefort)

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ASICS", version = "3.8")

adjclust

adjclust is an R package that implements a constrained version of hierarchical agglomerative clustering, in which each observation is associated to a position, and only adjacent clusters can be merged. Typical application fields in bioinformatics include Genome-Wide Association Studies or Hi-C data analysis, where the similarity between items is a decreasing function of their genomic distance. Taking advantage of this feature, the implemented algorithm is time and memory efficient.
adjclust has been partially developed as a 2017 GSoC project.

Role in the project: Author (Maintainer is Pierre Neuvial)

 install.packages("adjclust") 

NiLeDAM

NiLeDAM is an R package for dating monazites from measurements of triplets (U,Th,Pb) obtained by a microprobe technique. The implemented method is the one described in the article (Montel et al., 1996) and the package has been developed from the original programs made in basic language by Jean-Marc Montel (École Nationale Supérieure de Géologie, France). An example, kindly provided by Anne-Magali Seydoux-Guillaume is included in the package and is the one described in the article (Seydoux-Guillaume et al., 2012). Not maintained anymore
Monazite image by Aangelo (personal work) - licence GFDL or CC-BY-SA-3.0-2.5-2.0-1.0, via Wikimedia Commons

Role in the project: Maintainer and author

 install.packages("NiLeDAM", repos="http://R-Forge.R-project.org") 

			git clone https://github.com/tuxette/niledam.git