ade4 - Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Last updated 2 days ago
39 stars 9.28 score 6 dependencies 241 dependentsadespatial - Multivariate Multiscale Spatial Analysis
Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.
Last updated 2 days ago
34 stars 5.05 score 108 dependencies 1 dependentsnlstools - Tools for Nonlinear Regression Analysis
Several tools for assessing the quality of fit of a gaussian nonlinear model are provided.
Last updated 2 months ago
6 stars 4.99 score 0 dependencies 6 dependentsadephylo - Exploratory Analyses for the Phylogenetic Comparative Method
Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. The package contains functions to represent comparative data, compute phylogenetic proximities, perform multivariate analysis with phylogenetic constraints and test for the presence of phylogenetic autocorrelation. The package is described in Jombart et al (2010) <doi:10.1093/bioinformatics/btq292>.
Last updated 2 months ago
9 stars 4.94 score 88 dependencies 3 dependentsLDcorSV - Linkage Disequilibrium Corrected by the Structure and the Relatedness
Four measures of linkage disequilibrium are provided: the usual r^2 measure, the r^2_S measure (r^2 corrected by the structure sample), the r^2_V (r^2 corrected by the relatedness of genotyped individuals), the r^2_VS measure (r^2 corrected by both the relatedness of genotyped individuals and the structure of the sample).
Last updated 4 years ago
3.54 score 0 dependenciesadegraphics - An S4 Lattice-Based Package for the Representation of Multivariate Data
Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Last updated 2 months ago
9 stars 3.23 score 15 dependencies 5 dependentsMareyMap - Estimation of Meiotic Recombination Rates Using Marey Maps
Local recombination rates are graphically estimated across a genome using Marey maps.
Last updated 2 months ago
1 stars 3.20 score 0 dependenciesade4TkGUI - 'ade4' Tcl/Tk Graphical User Interface
A Tcl/Tk GUI for some basic functions in the 'ade4' package.
Last updated 2 months ago
2 stars 2.86 score 16 dependencieskissDE - Retrieves Condition-Specific Variants in RNA-Seq Data
Retrieves condition-specific variants in RNA-seq data (SNVs, alternative-splicings, indels). It has been developed as a post-treatment of 'KisSplice' but can also be used with user's own data.
Last updated 4 months ago
alternativesplicingdifferentialsplicingexperimentaldesigngenomicvariationrnaseqtranscriptomics
3 stars 2.05 score 187 dependenciesLifemapR - Data Visualisation on 'Lifemap' Tree
Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap <http://lifemap.univ-lyon1.fr/>. It takes as input a dataframe with at least a "taxid" column containing NCBI format TaxIds and allows to draw multiple layers with different visualisation tools.
Last updated 1 months ago
6 stars 1.92 score 72 dependenciesphylter - Detect and Remove Outliers in Phylogenomics Datasets
Analyzis and filtering of phylogenomics datasets. It takes an input either a collection of gene trees (then transformed to matrices) or directly a collection of gene matrices and performs an iterative process to identify what species in what genes are outliers, and whose elimination significantly improves the concordance between the input matrices. The methods builds upon the Distatis approach (Abdi et al. (2005) <doi:10.1101/2021.09.08.459421>), a generalization of classical multidimensional scaling to multiple distance matrices.
Last updated 2 months ago
phylogenetic-treesphylogeneticsphylogenomics
9 stars 1.86 score 42 dependenciesnlsMicrobio - Nonlinear Regression in Predictive Microbiology
Data sets and nonlinear regression models dedicated to predictive microbiology.
Last updated 2 months ago
1 stars 1.65 score 1 dependencies 1 dependentsInteratrix - Compute Chi-Square Measures with Corrections
Chi-square tests are computed with corrections.
Last updated 8 months ago
0.84 score 1 dependenciesCINID - Curculionidae INstar IDentification
Method for identifying the instar of Curculionid larvae from the observed distribution of the headcapsule size of mature larvae.
Last updated 4 years ago
0.00 score 0 dependencies