Metadata-Version: 1.1
Name: MAnorm
Version: 1.0.1
Summary: MAnorm -- A robust model for quantitative comparison of ChIP-Seq data sets, developed by Shao lab.
Home-page: http://bioinfo.sibs.ac.cn/shaolab/MAnorm/MAnorm.htm
Author: Hayden Sun
Author-email: sunhongduo@picb.ac.cn
License: GPLv3
Description-Content-Type: UNKNOWN
Description: ﻿# MAnorm
        ## 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
        
        > [MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets.](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-3-r16) Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ.   *Genome Biol. Mar 16;13(3):R16.*
        
        ## Installation
        ### pip
        ### conda
        ### setup.py
        
        ## Command
        manorm --p1 peak_file1 --p2 peak_file2 --r1 reads_file1 --r2 reads_file2 -o output_name
        
        **Note:** Using -h/--help for details.
        
        ## Peak Format
        Standard BED format and MACS xls format are supported. 
        Other supported format are listed below.
        
        ### 3-columns tab split format
        Chromosome Start End
        ```
        chr1  2345  4345
        chr1  3456  5456
        chr2  6543  8543 
        ```
        
        ### 4-columns tab split format
        Chromosome Start End Summit
        
        **Note:** The fourth column 'summit' is the relative position to 'start'.
         
        ```
        chr1  2345  4345  254
        chr1  3456  5456  127
        chr2  6543  8543  302
        ```
        
        ## Reads Format
        Only BED format are supported for now. More format will be embedded in the following updates. 
        
        ## License
        
        ## Contact
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
