All our software is open. A few of our major development projects are listed below.

Anduril (ANalysis of Data Using Rapid Integration of aLgorithms) is an opensource component-based workflow framework for systematic, flexible and efficient scientific data analysis, particularly in the field of high-throughput experiments in biomedical research. It includes components for expression, SNP, ChIP-seq and exon microarray analysis.


Anima is an image analysis workflow platfrom built on top of Anduril. Anima acts as a superplatform for the existing imaging applications, and can run components and software written many languages. In addition Anima provides API to the popular batch imaging environments: Fiji, CellProfiler and ImageMagick.


GROK (Genomic Region Operation Toolkit) is "Swiss Army knife" library for processing genomic interval data. GROK operates ongenomic regions, annotated chromosomal intervals that represent sequencing short reads, gene locations, ChIP-seq peaks or other genomic features. Applications of GROK include file format conversions, set operations, overlap queries, and filtering and transformation operations.


POIBM (Poisson batch correction trough sample matching) was developed for batch correction of RNA-seq data. The method finds both batch factors and matching samples between two sets of heterogeneous RNA-seq data, which can be used for correction. The data sets do not need to be prelabeled and no overlapping samples are required as the method relies on finding matching phenotypes among the various subgroups in the data.


DMML (Differential Methylation Maximum Likelihood) is method based on a latent stochastic model which allows comparing DNA methylomes at a single-nucleotide resolution between two or more tumor samples with different, unknown tumor purities. The method performs accurately without a normal cell control sample or prior tumor purity estimates, and accounts for spatially co-methylated cytosines, improving accuracy at lower coverage sites.