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NuPoP
Nucleosome positioning prediction
Mulcom
Differential expression and false discovery rate calculation through multiple comparison
ontoCAT
Ontology parsing
BHC
Bayesian Hierarchical Clustering
iSeq
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
btw, other interesting ones in BioC 2.6:
New sequence analysis tools address infrastructure (
GenomicRanges, Rsamtools, girafe); ChIP-seq (BayesPeak, CSAR, PICS); digital gene expression and RNA-seq (DESeq, goseq, segmentSeq); and motif discovery (MotIV, rGADEM).
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