sequenza: Copy Number Estimation from Tumor Genome Sequencing Data
Version 2.1.2

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
URL http://cbs.dtu.dk/biotools/sequenza/ Mailing list: https://groups.google.com/forum/#!forum/sequenza-user-group
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sequenza")

Popular man pages

baf.model.fit: Model fitting using Bayesian inference
CP.data: Example of cellularity and ploidy results
cp.plot: Plot log-posterior probability for the tested values of...
gc.norm: Normalize depth ratio values for GC-content bias
get.ci: Compute the confidence interval of cellularity and ploidy
VarScan2seqz: Import VarScan output files, for use with the Sequenza...
workflows: Sequenza convenience functions for standard analysis
See all...

All man pages Function index File listing

Man pages

baf.bayes: Model allele-specific copy numbers with specified cellularity...
baf.model.fit: Model fitting using Bayesian inference
chromosome.view: A graphical representation of multiple chromosomal features...
CP.data: Example of cellularity and ploidy results
cp.plot: Plot log-posterior probability for the tested values of...
example.seqz: Example "seqz" data
find.breaks: Segmentation of sequencing data using an allele-specific copy...
gc.norm: Normalize depth ratio values for GC-content bias
get.ci: Compute the confidence interval of cellularity and ploidy
model.points: Generate mutation frequency and depth ratio model point at...
mutation.table: Identify mutations
plotWindows: Plot a windowed chromosome
read.seqz: Read an seqz or acgt format file
theoretical.baf: Calculates cellularity-dependent model points
types.matrix: Creates a dataframe of type tags
VarScan2seqz: Import VarScan output files, for use with the Sequenza...
windowValues: Bins sequencing data for plotting
workflows: Sequenza convenience functions for standard analysis

Functions

CP.example Man page
VarScan2seqz Man page Source code
alternative.cp.solutions Source code
baf.bayes Man page Source code
baf.dbinom Source code
baf.dpois Source code
baf.model.fit Man page Source code
baf.model.points Source code
baf.ratio.model.fit Source code
chromosome.view Man page Source code
cp.plot Man page Source code
cp.plot.contours Man page Source code
depth.ratio.dbinom Source code
depth.ratio.dpois Source code
dt2 Source code
example.seqz Man page
expected.baf Source code
find.breaks Man page Source code
gc.norm Man page Source code
gc.sample.stats Man page Source code
genome.view Man page Source code
get.ci Man page Source code
mclapplyPb Source code
model.points Man page Source code
mufreq.bayes Man page Source code
mufreq.dbinom Source code
mufreq.dpois Source code
mufreq.model.fit Man page Source code
mut.fractions Source code
mutation.table Man page Source code
plotRawGenome Source code
plotWindows Man page Source code
read.acgt Man page Source code
read.seqz Man page Source code
segment.breaks Man page Source code
sequenza.extract Man page Source code
sequenza.fit Man page Source code
sequenza.results Man page Source code
sequenza2PyClone Source code
subclonal.matrix Source code
theoretical.baf Man page Source code
theoretical.depth.ratio Man page Source code
theoretical.mufreq Man page Source code
types.matrix Man page Source code
windowValues Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/sequenza.Rnw
inst/doc/sequenza.pdf
inst/doc/sequenza.R
exec
exec/sequenza-utils.py
NAMESPACE
NEWS
data
data/example.seqz.txt.gz
data/CP.example.RData
data/example.seqz.rda
R
R/graphics.R
R/model.R
R/workflows.R
R/analysis.R
R/next.R
R/bayes.R
R/misc.R
vignettes
vignettes/sequenza.Rnw
vignettes/sequenza.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/read.seqz.Rd
man/chromosome.view.Rd
man/cp.plot.Rd
man/plotWindows.Rd
man/model.points.Rd
man/baf.model.fit.Rd
man/gc.norm.Rd
man/example.seqz.Rd
man/workflows.Rd
man/types.matrix.Rd
man/find.breaks.Rd
man/baf.bayes.Rd
man/windowValues.Rd
man/VarScan2seqz.Rd
man/CP.data.Rd
man/get.ci.Rd
man/theoretical.baf.Rd
man/mutation.table.Rd
sequenza documentation built on May 19, 2017, 2:07 p.m.

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