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MSIseq specifications


Unique identifier OMICS_20471
Name MSIseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
IRanges, R(‚Č•3.2.0), R.utils, rJava, RWeka
Maintained Yes




No version available



  • person_outline Steve Rozen <>
  • person_outline Mini Huang <>

Publication for MSIseq

MSIseq citations


Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers

PMCID: 5906695
PMID: 29670109
DOI: 10.1038/s41467-018-03828-2

[…] for the hk cohort, only ebv and msi subtype status was available. the molecular subtypes of tumors from the icgc cohort were unavailable, but we identified one msi sample from the icgc cohort using msiseq., raw sequencing data was uniformly processed using the bcbio-nextgen pipeline (v0.9.3). briefly, sequencing reads were aligned to the human reference genome (hg19) using bwa. duplicated reads […]


Genomics of a pediatric ovarian fibrosarcoma. Association with the DICER1 syndrome

PMCID: 5818504
PMID: 29459759
DOI: 10.1038/s41598-018-21663-9

[…] these lines presented a dicer1 truncating mutation. interestingly, all of them presented also microsatellite instability (msi). for this reason, we analyzed the msi status in this patient using the msiseq package and found that the tumor indeed presented an msi-high profile, being negative to a pole-mutated phenotype. to validate this finding, we performed pcr and capillary electrophoresis […]

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MSIseq institution(s)
Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, , Singapore; Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore; Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore; Genome Institute of Singapore, A*STAR, Singapore, Singapore
MSIseq funding source(s)
Supported by the Duke-NUS Signature Research Programs funded by the Singapore Ministry of Health.

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