ePEST 1.0 – ChIP-exo Paired-ends Sequencing Processing Toolkit

ePEST 1.0

:: DESCRIPTION

ePEST leverages on the statistical powerful of r-scan for detecting binding peaks with son-3’-end reads and Chernoff inequality for identifying precise borders with exo-5′-end reads, respectively. The detected borders are further modelled as graphical components and classified into distinct border patterns based on their orientation and spacing.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ePEST

:: MORE INFORMATION

Citation

Ye Z, Chen Z, Sunkel B, Frietze S, Huang TH, Wang Q, Jin VX.
Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.
Nucleic Acids Res. 2016 Sep 19;44(16):7540-54. doi: 10.1093/nar/gkw659. Epub 2016 Jul 25. PMID: 27458208; PMCID: PMC5027512.

MACE 1.2 – Model-based Analysis of ChiP-exo

MACE 1.2

:: DESCRIPTION

MACE is a novel analysis framework to detect two binding borders of protein-DNA interactions from ChIP-exo data.

::DEVELOPER

Wei Li’s Computational Epigenomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 MACE

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Nov 10;42(20):e156. doi: 10.1093/nar/gku846. Epub 2014 Sep 23.
MACE: model based analysis of ChIP-exo.
Wang L, Chen J, Wang C, Uusküla-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W