MAnorm

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Introduction

ChIP-Seq is widely used to characterize genome-wide binding patterns of transcription factors and other chromatin-associated proteins. Although comparison of ChIP-Seq data sets is critical for understanding cell type-dependent and cell state-specific binding, and thus the study of cell-specific gene regulation, few quantitative approaches have been developed.

Here, we present a simple and effective method, MAnorm, for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators.

Citation

Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome biology. 2012 Mar 16;13(3):R16. <https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-3-r16>__

Documentation

To see the full documentation of MAnorm, please refer to: http://manorm.readthedocs.io

Installation

The latest release of MAnorm is available at PyPI <https://pypi.python.org/pypi/MAnorm>__:

::

$ pip install manorm

Or you can install MAnorm via conda:

::

$ conda install -c bioconda manorm

Galaxy Installation

MAnorm is also available on Galaxy_, you can incorporate MAnorm into your own Galaxy instance.

Please search and install MAnorm via the Galaxy Tool Shed_.

.. _Galaxy: https://galaxyproject.org .. _Galaxy Tool Shed: https://toolshed.g2.bx.psu.edu/view/haydensun/manorm

Basic Usage

::

$ manorm --p1 sample1_peaks.bed --p2 sample2_peaks.bed --r1 sample1_reads.bed --r2 sample2_reads.bed
--n1 name1 --n2 name2 -o output_dir

Note: Using -h/--help for the details of all arguments.

License

BSD 3-Clause License <https://github.com/shao-lab/MAnorm/blob/master/LICENSE>__