RamseyHAc (Histone acetylation) is a package of MATLAB M-files and data files is provided. The data files contain the feature tracks used for predicting TF binding sites, and the “ground truth” binding location data used to train the prediction model (both in MATLAB “.mat” file format). Also included is the file “GenomeRegions.bed” (in UCSC BED format) which describes the genome regions analyzed in this study. The M-files are the functions used to predict transcription factor binding, train the prediction model, and test the prediction model in a cross-validation framework.
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Bioinformatics. 2010 Sep 1;26(17):2071-5. doi: 10.1093/bioinformatics/btq405. Epub 2010 Jul 27.
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.
Ramsey SA1, Knijnenburg TA, Kennedy KA, Zak DE, Gilchrist M, Gold ES, Johnson CD, Lampano AE, Litvak V, Navarro G, Stolyar T, Aderem A, Shmulevich I.