sequenza: Copy Number Estimation from Tumor Genome Sequencing Data

Share:

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.

Author
Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Date of publication
2015-10-10 01:22:44
Maintainer
Francesco Favero <favero@cbs.dtu.dk>
License
GPL-3
Version
2.1.2
URLs

View on CRAN

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

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