HMCan 1.39 / HMCan-diff – Detection of (Differential) Chromatin Modifications in ChIP-seq data

HMCan 1.39 / HMCan-diff

:: DESCRIPTION

HMCan is Hidden Markov Model based tool that is developed to detect histone modification in cancer ChIP-seq data. It applies three correction steps to the data: copy number correction, GC bias correction and noise level correction.

HMCan-diff is a method designed specially to detect changes of histone modifications in ChIP-seq cancer samples or between a cancer sample and a normal control. HMCan-diff explicitly corrects for copy number bias as well as for other ChIP-seq technical biases such as GC-content and mappability biases, and variable levels of signal-to-noise in different samples. HMCan-diff uses a three state hidden Markov model to detect regions of differential histone modifications.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HMCan , HMCan-diff

:: MORE INFORMATION

Citation

Ashoor H, Louis-Brennetot C, Janoueix-Lerosey I, Bajic VB, Boeva V.
HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics.
Nucleic Acids Res. 2017 May 5;45(8):e58. doi: 10.1093/nar/gkw1319. PMID: 28053124; PMCID: PMC5416852.

Bioinformatics. 2013 Dec 1;29(23):2979-86. doi: 10.1093/bioinformatics/btt524. Epub 2013 Sep 9.
HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.
Ashoor H1, Hérault A, Kamoun A, Radvanyi F, Bajic VB, Barillot E, Boeva V.