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

dREG [GitHub]. Detection of active regulatory elements (promoters & enhancers) using GRO-seq and PRO-seq data.

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.