MEGSA specifications


Unique identifier OMICS_08312
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Jianxin Shi

Publication for MEGSA

MEGSA citations


A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co occurrence

Genome Biol
PMCID: 5162102
PMID: 27986087
DOI: 10.1186/s13059-016-1114-x

[…] sed for illustration is but a representative of a larger class of independence tests based on the same assumption. This class includes analytical approaches such as Fisher’s exact test, CoMEt [], and MEGSA [], but also permutation tests where gene alterations are uniformly shuffled across the tumors.We have presented a novel independence test based on assumptions that better match the reality of c […]


Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study

PLoS Med
PMCID: 5140047
PMID: 27923066
DOI: 10.1371/journal.pmed.1002162

[…] dies: TCGA, Broad Institute, and EAGLE, totaling 825 subjects. The analysis was performed for nonsynonymous mutations of 32 significantly mutated genes with mutation frequencies greater than 2% using MEGSA []. All reported p-values were adjusted for multiple comparison using 10,000 permutations. We identified four significant but overlapping MEGS, with EGFR included in three. The largest and most […]

MEGSA institution(s)
Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA

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