Our software packages that were previously hosted on Google Code have all been moved to GitHub, due to Google Code’s closure.
PLOS Computational Biology paper
We published a paper describing the Lemon-Tree software in the PLOS Computational Biology Software article collection:
Bonnet E, Calzone L, Michoel T. (2015) Integrative multi-omics module network inference with Lemon-Tree. PLoS Comput Biol 11(2): e1003983.
We posted a preprint titled “Integrative multi-omics module network inference with Lemon-Tree” on the arXiv. The preprint describes the current status of our module networks inference software Lemon-Tree and demonstrates how it can be used to identify cancer driver genes from large-scale copy number variation and gene expression datasets such as generated by The Cancer Genome Atlas. All of this is joint work with Eric Bonnet.
Source code and test data accompanying our paper Natural coordinate descent algorithm for L1-penalised regression in generalised linear models are now available from Google code.
kruX paper in BMC Bioinformatics
Our paper about the software tool kruX for performing millions of non-parametric ANOVA (Kruskal-Wallis) tests at once using matrix-multiplication methods has been published by BMC Bioinformatics. The final version is also available from the arXiv.
kruX preprint & software
A preprint of our paper kruX: Matrix-based non-parametric eQTL discovery is available from the arXiv. This paper describes a software tool called kruX for performing millions of non-parametric ANOVA (Kruskal-Wallis) tests at once using matrix-multiplication methods. kruX is about 3 orders of magnitude faster than performing these tests one-by-one, which makes a difference if you want to do billions of them!