CHANGES IN VERSION 1.30 ----------------------- NEW FEATURES o now has HOCOMOCO version 11, with all motifs classified, and queryable, by category ("core", "secondary") and reliability (A, B, C, D). CHANGES IN VERSION 1.24 ----------------------- NEW FEATURES o query method now flexible, with "andStrings", "orStrings", "notStrings" parameters The previous usage style is still supported. See man page. o associateTranscriptionFactors (with motifs) substantially faster CHANGES IN VERSION 1.20 ----------------------- NEW FEATURES o Now 13 sources, 52 organisms and 8369 motifs o New sources: HOCOMOCOv10, HOMER, jaspar2016, SwissRegulon o New methods: motifToGene, geneToMotif, associateTranscriptionFactors SIGNIFICANT USER-VISIBLE CHANGES o The new methods mentioned above provide both strict and permissive mapping from motifs to their cognate transcription factors, thus supporting reproducible regulatory network construction. CHANGES IN VERSION 1.5.9 ------------------------- NEW FEATURES o JASPAR_2014 added, with 592 motifs CHANGES IN VERSION 1.1.3 ------------------------- NEW FEATURES o 683 new motifs derived from DGF (digital genome footprinting) from the stamlab (http://www.stamlab.org/) added. Each is identified as either 'knownMotif' or 'novelMotif'