Month: October 2018

We are moving …. to bioC!

Dear all,

After 9 years hosted at the R CRAN we are migrating to bioconductor! It’s been a great first journey and we are grateful to the R CRAN for hosting our package. We are now ready for the next adventure.

Why are we moving?

  • It is our aspiration to empower computational and molecular biologists, which aligns with bioC vision.
  • We will be able to link with new experimentClass S4 objects and existing data packages using them in bioC, ranging from multi omics, microbiome and single cell.
  • We will be able to provide better vignettes and examples that will complement our website.

What has changed? What should I do? Should I panic?

So far we have allowed as little disruptions as possible, so the call of the functions and objects are the same. Gradually we will be adding more capabilities, which will grandly improve your usability (see above for the S4 class).

We are almost on bioC but the full acceptance is pending on the removal of mixOmics on the R CRAN. We fixed a few bugs, if you would like to install this new version:

The development version is now accessible on gitHub (feel free to fork / help* / comment on gitHub):

R>install_github("mixOmicsTeam/mixOmics")

Or alternatively, once we will be in bioConductor:

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

Then, business as usual!

* We would like to formally acknowledge the help of Lluís Revilla (Centre Esther Koplowitz, Barcelona) for helping us with setting up some testthat checks for our bioC version.

As we enter this new journey, we also thank you for this.
And also for this!

PS: a one-day microbiome workshop is scheduled in chilly Vancouver on November 6.

Nov 6 2018, Vancouver (microbiome)

Note: this workshop is primarily restricted to Microbiome Research Network students at UBC until Oct 22 when the registration will be open outside MRN if space is available.

About the Workshop 

The objective of this workshop is to introduce fundamental concepts of multivariate dimension reduction methodologies for biological data analysis. Each methodology presented during the course will be applied to case studies available in the R package mixOmics.

Methods for multivariate data analysis, data visualisation and microbial signature identification will be covered, as well as an introduction for multi-omics data integration.

You will learn how to:

  • Understand fundamental principles of multivariate projection-based dimension reduction techniques.
  • Perform statistical integration and feature selection using recently developed multivariate methodologies.
  • Apply those methods to high throughput biological studies, including your own studies.

This a special workshop offering as part of the Microbiome Research Network’s Exploring the Microcosmos Symposium. Tickets are available to MRN members only until Oct 22. At this time, additional tickets will be made publicly available if space is available.

 Pre-requisites

“Introduction to R”, EDUCE modules in MICB 301/405/425, or equivalent knowledge of R.

 MRN students

Microbiome Research Network (MRN) students should contact info.ecoscope@ubc.ca with 1) their name, 2) their PI’s name, and 3) the name of workshop to receive a registration code.

 Instructor

Dr Kim-Anh Lê Cao (University of Melbourne, Australia) was awarded her PhD in 2008 at Université de Toulouse, France. She then moved to Australia as a postdoctoral fellow at the University of Queensland, Brisbane. Since the beginning of her PhD Kim-Anh has initiated a wide range of valuable collaborative and research opportunities in both statistics and molecular biology. Her main research focus is on variable selection for biological data (`omics’ data) coming from different functional levels by the means of multivariate dimension reduction approaches. Since 2009, her team has been working on developing a statistical software dedicated to the integrative analysis of ‘omics’ data, to help researchers make sense of biological big data. Kim-Anh is a senior lecturer at the University of Melbourne (Melbourne Integrative Genomics, School of Mathematics and Statistics), and regularly runs statistical training workshops and short series seminars as well as mixOmics multi-day workshops.