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Article: CMT: a constrained multi-level thresholding approach for ChIP-Seq data analysis.

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Rezaeian I; Rueda L
PLoS ONE, 2014


10.1371/journal.pone.0093873.t005 Conceptual comparison of recently proposed methods for finding peaks in ChIP-Seq data.
Method Peak selection criteria Peak ranking Parameters
GLITR : Classification by height and relative enrichment Peak height and fold enrichment Target FDR, number of nearest neighbors for clustering
MACS Local region Poisson -value -value -value threshold, tag length, -fold for shift estimate
PeakSeq Local region binomial value value Target FDR
Quest v2.3 Height threshold, background ratio value KDE bandwidth, peaks height, sub-peak valley depth, ratio to background
SICER v1.02 value from random background model, enrichment relative to control value Window length, gap size, FDR (with control) or -Value (no control)
SiSSRs v1.4 sign change, threshold in region value FDR, threshold
T-PIC Local height threshold -value average fragment length, significance -value, minimum length of interval
Qeseq Local enrichment significance -value no parameter
CMT Height threshold and volume difference fold enrichment average fragment length, minimum and maximum region size, cut-off, minimum supported reads

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