signeR: Empirical Bayesian approach to mutational signature discovery
Version 1.2.1

The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variaton (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.

AuthorRafael Rosales, Rodrigo Drummond, Renan Valieris, Israel Tojal da Silva
Bioconductor views GenomicVariation SomaticMutation StatisticalMethod Visualization
Date of publicationNone
MaintainerRenan Valieris <renan.valieris@cipe.accamargo.org.br>
LicenseGPL-3
Version1.2.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("signeR")

Getting started

Package overview
README.md

Popular man pages

classify: Classify unknown samples
diffexp: Differential Exposure Analysis
genMatrix: count matrix and opportinity matrix generators
methods: SignExp class methods
plots: signeR plot functions
signeR: signeR
signeR-package: Empirical Bayesian approach to mutational signature discovery
See all...

All man pages Function index File listing

Man pages

classify: Classify unknown samples
diffexp: Differential Exposure Analysis
genMatrix: count matrix and opportinity matrix generators
methods: SignExp class methods
plots: signeR plot functions
signeR: signeR
signeR-package: Empirical Bayesian approach to mutational signature discovery
signexp-class: SignExp class

Functions

Average_exp Man page
Average_exp,SignExp-method Man page
Average_sign Man page
Average_sign,SignExp-method Man page
BICboxplot Man page Source code
Classify Man page
Classify,SignExp,character-method Man page
Comp_labels Source code
DiffExp Man page
DiffExp,SignExp,character-method Man page
EstimateParameters Source code
ExposureBarplot Man page
ExposureBarplot,SignExp-method Man page
ExposureBoxplot Man page
ExposureBoxplot,SignExp-method Man page
ExposureHeat Man page
ExposureHeat,SignExp-method Man page
GibbsSamplerCpp Source code
Median_exp Man page
Median_exp,SignExp-method Man page
Median_sign Man page
Median_sign,SignExp-method Man page
Normalize Man page
Normalize,SignExp-method Man page
Optimal_sigs Source code
Paths Man page
Paths,SignExp-method Man page
Reorder_mutations Man page
Reorder_mutations,SignExp,numeric-method Man page
Reorder_samples Man page
Reorder_samples,SignExp,numeric-method Man page
Reorder_signatures Man page
Reorder_signatures,SignExp,numeric-method Man page
SignExp Man page
SignExp-class Man page
SignExpConstructor Source code
SignHeat Man page
SignHeat,SignExp-method Man page
SignPlot Man page
SignPlot,SignExp-method Man page
eBayesNMF Source code
genCountMatrixFromVcf Man page Source code
genOpportunityFromGenome Man page Source code
genotypeIndexes Source code
getFirstGenoAltIndex Source code
isBadGeno Source code
isGenoIndexRef Source code
read.snv.context Source code
revcomp Source code
setMutations Man page
setMutations,SignExp-method Man page
setSamples Man page
setSamples,SignExp-method Man page
signeR Man page Source code
signeR-package Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/BICboxplot.R
R/Comp_labels.R
R/EstimateParameters.R
R/Optimal_sigs.R
R/RcppExports.R
R/SignExp.R
R/cpp_eBayesNMF.R
R/genMatrix.R
R/read.snv.context.R
R/signeR.R
README.md
build
build/partial.rdb
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/signeR-vignette.R
inst/doc/signeR-vignette.Rhtml
inst/doc/signeR-vignette.html
inst/extdata
inst/extdata/21_breast_cancers.mutations.txt
inst/extdata/21_breast_cancers.opportunity.txt
inst/extdata/example.bed
inst/extdata/example.vcf
man
man/classify.Rd
man/diffexp.Rd
man/genMatrix.Rd
man/methods.Rd
man/plots.Rd
man/signeR-package.Rd
man/signeR.Rd
man/signexp-class.Rd
src
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/gibbs_2.cpp
src/signeR_init.c
vignettes
vignettes/Model_selection_BICs.png
vignettes/signeR-vignette.Rhtml
signeR documentation built on May 20, 2017, 10:53 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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