BayesPrism. Try the (Beta!) BayesPrism web server!
Paper: Nature Cancer.
Source code here: BayesPrism [GitHub].

dREG Science Gateway. dREG now has a web server! Try it out.
Paper: Genome Research.
Source code here: dREG [GitHub].

RTFBSDB [GitHub]. Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
Paper: Bioinformatics.

AlleleHMM [GitHub]. Find allele-specific signal in distributed functional genomic data.
Paper: Nucleic Acids Research.

groHMM [Bioconductor]. Segment genomic data using hidden Markov models. Updated and maintained by the Kraus lab.

AffyTiling [Bioconductor]. Easy extraction of individual probes in Affymetrix tiling arrays.

Rgtsvm [GitHub]. R package for fitting and evaluating support vector machines (SVMs) using GPU hardware. e1071 compatible.

tfTarget [GitHub]. tfTarget is a unified framework that identifies the "TF -> TRE -> target gene" networks.