My group develops algorithms and software to facilitate the analysis and interpretation of large-scale genomic datasets. Source code is made freely available, mostly through GitHub. Follow the links below (sorted by most recent paper) for more information and please let us know if any of these tools helped you in your research.
- Lvreml – Restricted maximum-likelihood method for learning latent variance components in gene expression data with known and unknown confounders. [Homepage] [G3 2021]
- Findr – Fast Inference of Networks from Directed Regulations. [Homepage]
[PLOS Comp Biol 2017] [Book chapter 2018] [IJMS 2018][Front Genet 2019] [Mol Omics 2021] - GraphFeatureAutoencoder – a graph feature autoencoder for expression value prediction and imputation [Homepage] [BMC Bioinfo 2021]
- Lemon-Tree – Learning Module Networks version 3. [Homepage]
[PLOS Comp Biol 2017] [Book chapter 2018][Bioinformatics 2019] - Bayonet – Matlab implementation of an analytic solution and stationary phase approximation for the Bayesian lasso and elastic net. [Homepage] [NeurIPS 2018]
- Lassopv – R package for obtaining p-values in Lasso regression. [homepage][arXiv 2017]
- Glmnat – Matlab implementation of a natural coordinate descent algorithm for L1-penalised regression in generalized linear models. [Homepage] [CSDA 2016]
- kruX – A Matlab/R/Python tool for simultaneously performing millions of non-parametric ANOVA (Kruskal-Wallis) tests using matrix-multiplication methods. [Homepage] [BMC Bioinfo 2014]
- ISMA – The Index-based Subgraph Matching Algorithm. [Homepage] [PLOS One 2013]
- SCHype – A Java command line tool for spectral clustering in hypergraphs. [homepage] [Phys Rev E 2012]
- TwixTrix – A Matlab and R tool for context-specific transcriptional regulatory network inference. [Homepage] [Bioinformatics 2012]
- Network Motif Clustering Toolbox – a Matlab toolbox for clustering topological motifs in integrated networks. [Homepage] [Mol BioSyst 2011]
- CyClus3D – a Cytoscape plugin for clustering network motifs in integrated networks. [Homepage] [Bioinformatics 2011]
- LeMoNe – a Java package for learning module networks from gene expression data. [Homepage]
[paper] [paper] [paper] [paper] [paper] [paper] [paper] [paper] - Pathicular – a Cytoscape plugin for identifying regulatory path motifs in integrated networks. [Homepage] [Genome Biol 2010]
- GaneSh – a Java package for 2-way clustering of gene expression data using a Gibbs sampling method. Ganesh is also part of the Lemon-Tree package. [Homepage] [Bioinformatics 2008]
- MatrixClust – a Matlab toolbox for fuzzy clustering of a symmetric matrix, typically the weighted adjacency matrix of an undirected network. [Homepage] [Bioinformatics 2009] [Bioinformatics 2008]
- D-MiRaGe – a Matlab toolbox for performing ground state and time-dependent Density Matrix Renormalization Group computations for one-dimensional quantum spin systems which need not be translation invariant. [Homepage] [J Phys A 2008] [New J Phys 2010]
- DNAmelt – a Matlab toolbox to compute DNA melting properties using a helicoidal transfer matrix model. [Homepage] [Phys Rev E 2006]
Resources
The following are links to repositories that contain supplementary data and scripts to reproduce analyses in some of our papers (sorted by most recent paper).
- FindrCausalInferenceOnYeast – Python code to reproduce the causal networks inferred from differential gene expression in yeast. [Homepage][BioRxiv 2020]
- GraphFeatureAutoencoder – Code to implement graph feature auto-encoders to predict expression data using biological networks. [Homepage][arXiv 2020]
- VSG analysis – Scripts for the analysis of a PacBio dataset of expressed antigen diversity in T. brucei infections. [Homepage] [PLOS Path 2019]
- DHSgen – A list of high-confidence predicted interactions between regulatory genome regions and their target genes. [Homepage] [arXiv 2014]
- RNA regulon-omics – A portal for molecular biologists who wish to design detailed hypotheses from a large-scale, top-down analysis of posttranscriptional regulation in yeast. [Homepage] [NAR 2011]