Software
![](images/BayesPrism-Logo-Small.png)
BayesPrism. Try the (Beta!) BayesPrism web server!
Paper: Nature Cancer.
Source code here: BayesPrism [GitHub].
![](images/dREG-gateway-logo-muted-small.png)
dREG Science Gateway. dREG now has a web server! Try it out.
Paper: Genome Research.
Source code here: dREG [GitHub].
![](images/rtfbsdb.png)
RTFBSDB [GitHub]. Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
Paper: Bioinformatics.
![](images/AlleleHMM-small.png)
AlleleHMM [GitHub]. Find allele-specific signal in distributed functional genomic data.
Paper: Nucleic Acids Research.
![](images/groHMM.png)
groHMM [Bioconductor]. Segment genomic data using hidden Markov models. Updated and maintained by the Kraus lab.
![](images/AffyTiling.png)
AffyTiling [Bioconductor]. Easy extraction of individual probes in Affymetrix tiling arrays.
![](images/Rgtsvm.png)
Rgtsvm [GitHub]. R package for fitting and evaluating support vector machines (SVMs) using GPU hardware. e1071 compatible.
![](images/dREG.Preprint.png)
tfTarget [GitHub]. tfTarget is a unified framework that identifies the "TF -> TRE -> target gene" networks.