MAnorm protocols

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description
MAnorm computational protocol

MAnorm specifications

Information


Unique identifier OMICS_00467
Name MAnorm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB, R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainers


  • person_outline Stuart Orkin <>
  • person_outline David Waxman <>

Publication for MAnorm

MAnorm IN pipelines

 (2)
2016
PMCID: 5063967
PMID: 27694846
DOI: 10.1038/ncomms13018

[…] enriched in chip-seq tags were identified by model-based analysis for chip-seq (macs2, version 2.1.0.20150603; parameters: --nomodel, -p 0.01)60. differential peaks were identified using ‘manorm' method61. for this method, the normalized m value (m=log2 (read density in c2h4 treated sample per read density in air treated sample) represents log2-transformed fold changes of enrichment […]

2013
PMCID: 3687337
PMID: 23795291
DOI: 10.7554/eLife.00633.024

[…] introns, and intergenic regions (outside of these defined regions) was calculated. identified peaks were then mapped to refseq annotated genes (pruitt et al., 2004) for downstream analyses. to use ‘manorm’ normalization (shao et al., 2012), one assumes that the true intensities of most common peaks are the same between two chip-seq samples. this assumption is valid when the binding regions […]

MAnorm institution(s)
Departments of Pediatric Oncology and Computational Biology, DanaFarber Cancer Institute, Boston, MA, USA; Division of Pediatric Hematology-Oncology, The Karp Family Research Laboratories, Children’s Hospital, Boston, MA, USA; Division of Cell and Molecular Biology, Department of Biology, Boston University, Boston, MA, USA; Harvard Stem Cell Institute and the Howard Hughes Medical Institute, Children’s Hospital, Boston, MA, USA

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