PICS identifies binding event locations by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model.
We present a novel approach based on large margin learning that combines accurate splice site predictions with common sequence alignment techniques. By solving a convex optimization problem, our algorithm -- called PALMA -- tunes the parameters of the model such that true alignments sco...
Detects fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq studies and characterize fusion junctions at base-pair resolution.
The R/Bioconductor package girafe facilitates the functional exploration of alignments of sequence reads from next-generation sequencing data to a genome. It allows users to investigate the genomic intervals together with the aligned reads and to work with, visualise and export these in...
SeqCons is an open source consensus computation program for Linux and Windows. The algorithm can be used for de novo and reference-guided sequence assembly.
Frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure; in this structure, each “child” sequence is considered to be stochastically derived from its more abundant “parent” sequence wi...
MethMarker facilitates the design of DNA methylation assays for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight and MSP. It also implements a systematic workflow for design, optimization and (computational) validation of DNA methylation biomarkers. This workflow starts from...