signeR: Empirical Bayesian approach to mutational signature discovery

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
Date of publicationNone
MaintainerRenan Valieris <renan.valieris@cipe.accamargo.org.br>
LicenseGPL-3
Version1.0.1

View on Bioconductor

Functions

Average_exp Man page
Average_exp,SignExp-method Man page
Average_sign Man page
Average_sign,SignExp-method Man page
BICboxplot Man page
Classify Man page
Classify,SignExp,character-method Man page
DiffExp Man page
DiffExp,SignExp,character-method Man page
ExposureBarplot Man page
ExposureBarplot,SignExp-method Man page
ExposureBoxplot Man page
ExposureBoxplot,SignExp-method Man page
ExposureHeat Man page
ExposureHeat,SignExp-method Man page
genCountMatrixFromVcf Man page
genOpportunityFromGenome Man page
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
Paths Man page
Paths,SignExp-method Man page
Reorder Man page
Reorder,SignExp,numeric-method Man page
setMutations Man page
setMutations,SignExp-method Man page
setSamples Man page
setSamples,SignExp-method Man page
signeR Man page
signeR-package Man page
SignExp Man page
SignExp-class Man page
SignHeat Man page
SignHeat,SignExp-method Man page
SignPlot Man page
SignPlot,SignExp-method Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.