MSIseq statistics

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Tool usage distribution map

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Associated diseases

Associated diseases

MSIseq specifications

Information


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
Requirements
IRanges, R(≥3.2.0), R.utils, rJava, RWeka
Maintained Yes

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Documentation


Maintainers


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

Publication for MSIseq

MSIseq in pipeline

2018
PMCID: 5818504
PMID: 29459759
DOI: 10.1038/s41598-018-21663-9

[…] by exon and using a breakpoint threshold of 1.5. translocations were assessed using delly, using standard parameters., msi status was infered from raw tumoral snv and microindels data using the msiseq package, using the author´s 526 tumoral exomes training database. msi was validated using a panel of 5 markers that include bat25, bat26, nr21, nr22 and nr24; pcr of 5 markers in germinal […]


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MSIseq in publications

 (2)
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 […]

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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