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 |
Inferred neuron-electrophysiology data values
Neuron Type |
Neuron Description |
Ephys Prop |
Extracted Value |
Standardized Value |
Content Source |