sequenza: Copy Number Estimation from Tumor Genome Sequencing Data

Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.

AuthorFrancesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Date of publication2015-10-10 01:22:44
MaintainerFrancesco Favero <favero@cbs.dtu.dk>
LicenseGPL-3
Version2.1.2
http://cbs.dtu.dk/biotools/sequenza/
Mailing list: https://groups.google.com/forum/#!forum/sequenza-user-group

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Files in this package

sequenza
sequenza/inst
sequenza/inst/CITATION
sequenza/inst/doc
sequenza/inst/doc/sequenza.Rnw
sequenza/inst/doc/sequenza.pdf
sequenza/inst/doc/sequenza.R
sequenza/exec
sequenza/exec/sequenza-utils.py
sequenza/NAMESPACE
sequenza/NEWS
sequenza/data
sequenza/data/example.seqz.txt.gz
sequenza/data/CP.example.RData
sequenza/data/example.seqz.rda
sequenza/R
sequenza/R/graphics.R sequenza/R/model.R sequenza/R/workflows.R sequenza/R/analysis.R sequenza/R/next.R sequenza/R/bayes.R sequenza/R/misc.R
sequenza/vignettes
sequenza/vignettes/sequenza.Rnw
sequenza/vignettes/sequenza.bib
sequenza/MD5
sequenza/build
sequenza/build/vignette.rds
sequenza/DESCRIPTION
sequenza/man
sequenza/man/read.seqz.Rd sequenza/man/chromosome.view.Rd sequenza/man/cp.plot.Rd sequenza/man/plotWindows.Rd sequenza/man/model.points.Rd sequenza/man/baf.model.fit.Rd sequenza/man/gc.norm.Rd sequenza/man/example.seqz.Rd sequenza/man/workflows.Rd sequenza/man/types.matrix.Rd sequenza/man/find.breaks.Rd sequenza/man/baf.bayes.Rd sequenza/man/windowValues.Rd sequenza/man/VarScan2seqz.Rd sequenza/man/CP.data.Rd sequenza/man/get.ci.Rd sequenza/man/theoretical.baf.Rd sequenza/man/mutation.table.Rd

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