We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNASeq data, we show that our method is more accurate than previous methods. Our improved accuracy is the res...
Crossbow is a cloud-computing software tool that combines the aligner BOWTIE and the SNP caller SOAPsnp.
Crossbow is a cloud-computing software tool that combines the aligner BOWTIE and the SNP caller SOAPsnp.
Ibis (Improved base identification system), is an accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. Ibis is faster and makes fewer assumptions about chemistry and technology...
Differential Binding Analysis of ChIP-Seq peak data Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
Collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations
Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to i...