A physical model for tiling array analysis

Investigation of Submerged Vanes Array for Sediment Control at Intake Using a Physical Model

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge

MOTIVATION Large-scale tiling array experiments are becoming increasingly common in genomics. In particular, the ENCODE project requires the consistent segmentation of many different tiling array datasets into 'active regions' (e.g. finding transfrags from transcriptional data and putative binding sites from ChIP-chip experiments). Previously, such segmentation was done in an unsupervised fashi...

Investigation of Submerged Vanes Array for Sediment Control at Intake Using a Physical Model

The waveTiling package

In this waveTiling package vignette the package’s main functionalities to conduct a tiling array trancriptome analysis are illustrated. The package contains an implementation of the basic wavelet-based functional model introduced in [1], and its extensions towards more complex designs described in [3]. The leaf development data set [2] contains genome-wide expression data measured for six devel...

biomvRCNS : Copy Number study and Segmentation for multivariate biological data

With high throughput experiments like tiling array and NGS, researchers are looking for continuous homogeneous segments or signal peaks, which would represent chromatin states, methylation ratio, transcripts or genome regions of deletion and amplification. While in a normal experimental set-up, these profiles would be generated for multiple samples or conditions with replicates. In the package ...