signeR: signeR

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.

Author
Rafael Rosales, Rodrigo Drummond, Renan Valieris, Israel Tojal da Silva
Date of publication
None
Maintainer
Renan Valieris <renan.valieris@cipe.accamargo.org.br>
License
GPL-3
Version
1.0.0

View on Bioconductor

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
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("signeR")}
signexp-class
SignExp class

Files in this package

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