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sequenza (version 2.1.1)

Copy Number Estimation from Tumor Genome Sequencing Data

Description

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.

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Version

Install

install.packages('sequenza')

Monthly Downloads

4

Version

2.1.1

License

GPL-3

Maintainer

Francesco Favero

Last Published

January 27th, 2015

Functions in sequenza (2.1.1)

baf.bayes

Model allele-specific copy numbers with specified cellularity and ploidy parameters
cp.plot

Plot log-posterior probability for the tested values of cellularity and ploidy
chromosome.view

A graphical representation of multiple chromosomal features in parallel
baf.model.fit

Model fitting using Bayesian inference
sequenza

Sequenza convenience functions for standard analysis
example.seqz

Example seqz data
windowValues

Bins sequencing data for plotting
plotWindows

Plot a windowed chromosome
read.seqz

Read an seqz or acgt format file
CP.example

Example of cellularity and ploidy results
gc.sample.stats

Normalize depth ratio values for GC-content bias
theoretical.baf

Calculates cellularity-dependent model points
model.points

Generate mutation frequency and depth ratio model point at given cellularity and ploidy value
types.matrix

Creates a dataframe of type tags
find.breaks

Segmentation of sequencing data using an allele-specific copy number algorithm
get.ci

Compute the confidence interval of cellularity and ploidy
VarScan2seqz

Import VarScan output files, for use with the Sequenza algorithm.
mutation.table

Identify mutations