-
Recent Posts
Recent Comments
Archives
- June 2024
- May 2024
- October 2023
- March 2023
- January 2023
- August 2022
- November 2021
- September 2021
- June 2021
- May 2021
- March 2020
- September 2019
- April 2019
- February 2019
- January 2019
- October 2018
- June 2018
- April 2018
- March 2018
- February 2018
- November 2017
- October 2017
- September 2017
- August 2017
- June 2017
- May 2017
- February 2017
- October 2016
- September 2016
- August 2016
- July 2016
- June 2016
- May 2016
- March 2016
- November 2015
- September 2015
- August 2015
- July 2015
- May 2015
- April 2015
- November 2014
- October 2014
- September 2014
- August 2014
- June 2014
- October 2013
- February 2013
- May 2012
- April 2012
- August 2011
- June 2011
- March 2011
- November 2010
- September 2010
- August 2010
- May 2010
- December 2009
Categories
Meta
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
Comments Off on Φ-Space: Continuous phenotyping of single-cell multi-omics data
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
Comments Off on Microbial network inference for longitudinal microbiome studies with LUPINE
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
Comments Off on General presentation about mixOmics
(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
Comments Off on (s)IPCA
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
Comments Off on New methods: multilevel analyses
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
Comments Off on Web-interface
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
Comments Off on New Graphics: network & cim
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
Comments Off on New Function: (s)PCA added
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
Comments Off on New function: plot.valid