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SUMMARY Circular layout is an efficient way for the visualization of huge amounts of genomic information. Here we present the circlize package, which provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that(More)
MOTIVATION High-throughput molecular genetics methods allow the collection of data about the expression of genes at different time points and under different conditions. The challenge is to infer gene regulatory interactions from these data and to get an insight into the mechanisms of genetic regulation. RESULTS We propose a model for genetic regulatory(More)
The observed motion of subcellular particles in fluorescence microscopy image sequences of live cells is generally a superposition of the motion and deformation of the cell and the motion of the particles. Decoupling the two types of movements to enable accurate classification of the particle motion requires the application of registration algorithms. We(More)
MOTIVATION The wide use of DNA microarrays for the investigation of the cell transcriptome triggered the invention of numerous methods for the processing of microarray data and lead to a growing number of microarray studies that examine the same biological conditions. However, comparisons made on the level of gene lists obtained by different statistical(More)
We present an intensity-based nonrigid registration approach for the normalization of 3-D multichannel microscopy images of cell nuclei. A main problem with cell nuclei images is that the intensity structure of different nuclei differs very much; thus, an intensity-based registration scheme cannot be used directly. Instead, we first perform a segmentation(More)
Modern developments in time-lapse fluorescence microscopy enable the observation of a variety of processes exhibited by viruses. The dynamic nature of these processes requires the tracking of viruses over time to explore spatial-temporal relationships. In this work, we developed deterministic and probabilistic approaches for multiple virus tracking in(More)
The evaluation of fluorescence microscopy images acquired in high-throughput cell phenotype screens constitutes a substantial bottleneck and motivates the development of automated image analysis methods. Here we introduce a computational scheme to process 3D multi-cell time-lapse images as they are produced in large-scale RNAi experiments. We describe an(More)
SUMMARY We present RNAither, a package for the free statistical environment R which performs an analysis of high-throughput RNA interference (RNAi) knock-down experiments, generating lists of relevant genes and pathways out of raw experimental data. The library provides a quality assessment of the signal intensities, as well as a broad range of options for(More)
MOTIVATION Alternative splicing is central for cellular processes and substantially increases transcriptome and proteome diversity. Aberrant splicing events often have pathological consequences and are associated with various diseases and cancer types. The emergence of next-generation RNA sequencing (RNA-seq) provides an exciting new technology to analyse(More)