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Last edited by Istvan Ladunga

Peak Calling Tools 2016-09-09

  • SPP
  • MACS2
  • Cexor (in R) ? Pedro says no.
  • Peakranger
  • JAMM not now
  • GEM
  • BayesPeak (in R) (Cairns, Spyrou et al. 2011)
  • CCAT (Xu, Handoko et al. 2010)

4 (6) Cell lines or cell types K562 cells (human) and their mouse analog, MEL H1-hESC embryonic stem cells (human), and E14 ES (mouse) Possibly, GM12878 lymphoblastoid cells (human), and their mouse analog, CH12.LX

7 Transcription factors FOXA GABP MYC MAX KAT2A NRSF STAT

5 Histone modifications

H3K36me3 H3K4me3 H3K27ac H3K27me3 H3K4me1

hg19: 34 experiments total

mm9: 3 cell types: CH12.LX, ES-E14, MEL

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