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MutationalPatterns specifications

Information


Unique identifier OMICS_14060
Name MutationalPatterns
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Somatic mutation catalogues
Input format VCF
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 0.99.6
Stability Stable
Requirements
BiocInstaller, devtools
Maintained Yes

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Documentation


Maintainer


  • person_outline Edwin Cuppen

Publication for MutationalPatterns

MutationalPatterns citations

 (4)
library_books

Highly similar genomic landscapes in monoclonal B cell lymphocytosis and ultra stable chronic lymphocytic leukemia with low frequency of driver mutations

2018
Haematologica
PMCID: 5927998
PMID: 29449433
DOI: 10.3324/haematol.2017.177212

[…] ll major differences were identified between MBL/CLL samples and PMN samples with the former group exhibiting mainly C>T mutations at NpCpG trinucleotides (P<0.05 for ultra-stable CLL and HC-MBL).The MutationalPatterns package was used to delineate the mutational signatures in our cohort. Mutational patterns identified in the MBL/CLL samples resembled those reported by Puente et al.; this finding […]

library_books

MutationalPatterns: comprehensive genome wide analysis of mutational processes

2018
Genome Med
PMCID: 5922316
PMID: 29695279
DOI: 10.1186/s13073-018-0539-0

[…] e original and reconstructed mutation profiles were comparable for MutationalPatterns (mean α = 0.978, mean RSS = 1.38e-03) and deconstructSigs (mean α = 0.977, mean RSS = 1.40e-03). Importantly, the MutationalPatterns analysis runtime is approximately 400 times faster compared with deconstructSigs (Additional file : Figure S2C). […]

library_books

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

2018
Nat Commun
PMCID: 5824957
PMID: 29476074
DOI: 10.1038/s41467-018-03244-6

[…] The distribution of somatic mutations across the human genome (Supplementary Fig. ) was visualized using the function “plot_rainfall” of the R-package MutationalPatterns,. The observed and expected numbers of mutations in the different genomic regions (Fig. ) were analyzed using the function “genomic_distribution”. Input data were the somatic mutati […]

library_books

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

2018
Nat Commun
PMCID: 5750210
PMID: 29296022
DOI: 10.1038/s41467-017-02424-0

[…] el model. The copy number alterations (CNAs) identified using exome-sequencing data were concordant to those in the same samples by using Affymetrix SNP Array. LOH events were derived using VarScan2. MutationalPatterns (https://doi.org/10.1101/071761) was used to infer the contribution of published mutational signatures. […]

Citations

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MutationalPatterns institution(s)
Department of Genetics, Center for Molecular Medicine, Cancer Genomics Netherlands, University Medical Center Utrecht, Utrecht, Netherlands
MutationalPatterns funding source(s)
This work was financially supported by the NWO Gravitation Program Cancer Genomics.nl and the NWO/ZonMW Zenith project 93512003.

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