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

View on CRAN

Functions

baf.bayes Man page
baf.model.fit Man page
chromosome.view Man page
CP.example Man page
cp.plot Man page
cp.plot.contours Man page
example.seqz Man page
find.breaks Man page
gc.norm Man page
gc.sample.stats Man page
genome.view Man page
get.ci Man page
model.points Man page
mufreq.bayes Man page
mufreq.model.fit Man page
mutation.table Man page
plotWindows Man page
read.acgt Man page
read.seqz Man page
segment.breaks Man page
sequenza.extract Man page
sequenza.fit Man page
sequenza.results Man page
theoretical.baf Man page
theoretical.depth.ratio Man page
theoretical.mufreq Man page
types.matrix Man page
VarScan2seqz Man page
windowValues Man page

Files

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

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

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