Other packages > Find by keyword >

mutSignatures  

Decipher Mutational Signatures from Somatic Mutational Catalogs
View on CRAN: Click here


Download and install mutSignatures package within the R console
Install from CRAN:
install.packages("mutSignatures")

Install from Github:
library("remotes")
install_github("cran/mutSignatures")

Install by package version:
library("remotes")
install_version("mutSignatures", "2.1.1")



Attach the package and use:
library("mutSignatures")
Maintained by
Damiano Fantini
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-01-24
Latest Update: 2020-11-09
Description:
Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes. This computational framework is aimed at deciphering DNA mutational signatures operating in cancer. The framework includes modules that support raw data import and processing, mutational signature extraction, and results interpretation and visualization. The framework accepts widely used file formats storing information about DNA variants, such as Variant Call Format files. The framework performs Non-Negative Matrix Factorization to extract mutational signatures explaining the observed set of DNA mutations. Bootstrapping is performed as part of the analysis. The framework supports parallelization and is optimized for use on multi-core systems. The software was described by Fantini D et al (2020) and is based on a custom R-based implementation of the original MATLAB WTSI framework by Alexandrov LB et al (2013) .
How to cite:
Damiano Fantini (2017). mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs. R package version 2.1.1, https://cran.r-project.org/web/packages/mutSignatures. Accessed 30 Jan. 2025.
Previous versions and publish date:
1.2 (2017-01-24 08:12), 2.0.1 (2020-07-06 11:20)
Other packages that cited mutSignatures R package
View mutSignatures citation profile
Other R packages that mutSignatures depends, imports, suggests or enhances
Complete documentation for mutSignatures
Functions, R codes and Examples using the mutSignatures R package
Some associated functions: addWeak . alexaNMF . as.data.frame-mutSignExposures-method . as.data.frame-mutationCounts-method . as.data.frame-mutationSignatures-method . as.list-mutFrameworkParams-method . as.list-mutationSignatures-method . as.matrix-mutationCounts-method . as.mutation.counts . as.mutation.signatures . as.mutsign.exposures . attachContext . attachMutType . bootstrapCancerGenomes . cbind2 . chihJenNMF . coerceObj-methods . countMutTypes . custom_cssls . custom_fcnnls . decipherMutationalProcesses . deconvoluteMutCounts . evaluateStability . extractSignatures . extractXvarlinkData . filterOutIterations . filterSNV . frequencize . getCosmicSignatures . getCounts . getFwkParam . getMutationTypes . getSampleIdentifiers . getSignatureIdentifiers . getTestRunArgs . importVCFfiles . leadZeros . matchSignatures . msigPlot . mutFrameworkParams-class . mutFrameworkParams-show . mutSigData . mutSignExposures-class . mutSignExposures-show . mutSignatures-package . mutationCounts-class . mutationCounts-show . mutationSignatures-class . mutationSignatures-show . plotMutTypeProfile . plotSignExposures . prelimProcessAssess . processVCFdata . removeMismatchMut . removeWeak . resolveMutSignatures . revCompl . setFwkParam . setMutClusterParams . silhouetteMLB . simplifySignatures . sortByMutations . sub-mutSignExposures-numeric-ANY-ANY-method . sub-mutationCounts-numeric-ANY-ANY-method . sub-mutationSignatures-numeric-ANY-ANY-method . table2df . 
Some associated R codes: s01_all_classes.R . s02_all_methods.R . s03_all_functions.R . s04_all_extra.R .  Full mutSignatures package functions and examples
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

kesernetwork  
Visualization of the KESER Network
A shiny app to visualize the knowledge networks for the code concepts. Using co-occurrence matrices ...
Download / Learn more Package Citations See dependency  
fastmit  
Fast Mutual Information Based Independence Test
A mutual information estimator based on k-nearest neighbor method proposed by A. Kraskov, et al. (20 ...
Download / Learn more Package Citations See dependency  
cinaR  
A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data analyses. This package combi ...
Download / Learn more Package Citations See dependency  
GGMncv  
Gaussian Graphical Models with Nonconvex Regularization
Estimate Gaussian graphical models with nonconvex penalties , including ...
Download / Learn more Package Citations See dependency  
convertid  
Convert Gene IDs Between Each Other and Fetch Annotations from Biomart
Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in conve ...
Download / Learn more Package Citations See dependency  
WtTopsis  
Weighted Method for Multiple-Criteria Decision Making
Evaluation of alternatives based on multiple criteria using weighted technique for Order preference ...
Download / Learn more Package Citations See dependency  

23,580

R Packages

204,057

Dependencies

63,980

Author Associations

23,581

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA