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Category Archives: Methods
Φ-Space: Continuous phenotyping of single-cell multi-omics data
We have developed a new PLS method for cell type continuous annotation of single cells, now in preprint! Φ-Space addresses numerous challenges faced by state-of-the-art automated annotation methods: to identify continuous and out-of-reference cell states, to deal with batch effects … Continue reading
Posted in Methods, Publications, Updates, webinar
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PCA and PLS-DA
These two recordings were part of a presentation to WEHI for their postgraduate lecture series for a diverse audience. In the PCA presentation (18 min), we explain the concept of linear combination of variables (components) and useful graphical outputs such … Continue reading
Microbial network inference for longitudinal microbiome studies with LUPINE
Our latest method based on PLS to infer microbial networks across time is now in preprint! LUPINE is a PLS-based method that combines dimension reduction, and partial correlations to infer associations between taxa. LUPINE takes into account information across time … Continue reading
Posted in Methods, News, Publications
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General presentation about mixOmics
A new general presentation about mixOmics is available (and should be updated for major update of the package) in the [intlink id=”204″ type=”page”]Presentation Section[/intlink]. Lê Cao K.-A. Unravelling `omics’ data with the mixOmics R package, Illustration on several studies. General presentation on mixOmics … Continue reading
Posted in Case Studies, Graphics, Methods, News, Publications, Research
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(s)IPCA
Independent Principal Component Analysis (IPCA) In some case studies, we have identified some limitations when using PCA: PCA assumes that gene expression follows a multivariate normal distribution and recent studies have demonstrated that microarray gene expression measurements follow instead a … Continue reading
Posted in Case Studies, Graphics, Methods, News, Publications, Research
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New methods: multilevel analyses
A multilevel approach has been added for cross-over design experiments (up to two cross factors), in collaboration with A/Prof B. Liquet (Universite de Bordeaux, France). This approach takes into account the complex structure of repeated measurements from different assays, where different treatments are applied … Continue reading
Posted in Case Studies, Graphics, Methods, News, Publications, Research
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Web-interface
R package and Methods: IPCA and sparse IPCA functions have been implemented (as well as their associated S3 functions). IPCA stands for Principal Component Analysis with Independent Loadings. It is a combination of the advantages of both PCA and Independent … Continue reading
Posted in Case Studies, Graphics, Methods, News, Publications, Research
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New Graphics: network & cim
New S3 method network and cim for results from PLS model New code for the valid function to PLS-DA and SPLS-DA models validation The S3 method plot.valid was modified to display graphical results from valid function for PLS-DA and SPLS-DA models cim and network functions were … Continue reading
Posted in Case Studies, Graphics, Methods, News, Publications, Research
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New Function: (s)PCA added
New function pca and spca are now available to perform Principal Component Analysis (PCA) and sparse PCA for variable selection The S3 methods plotVar, plot3dVar, plotIndiv, plot3dIndiv were modified to generate graphical results for pca and spca
Posted in Case Studies, Graphics, Methods, News, Publications, Research
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New function: plot.valid
New function plot.valid to display the results of the valid function New code for imgCor function for a nicer representation of the correlation matrices In predict function the argument ‘method’ were replaced by method = c(“max.dist”, “class.dist”, “centroids.dist”, “mahalanobis.dist”) The arguments dendrogram, ColSideColors and RowSideColors were added to the cim … Continue reading
Posted in Case Studies, Graphics, Methods, News, Publications, Research
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