exomeCopy: Copy number variant detection from exome sequencing read depth

Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("exomeCopy")
AuthorMichael Love
Bioconductor views CopyNumberVariation Genetics Sequencing
Date of publicationNone
MaintainerMichael Love <michaelisaiahlove@gmail.com>
LicenseGPL (>= 2)
Version1.22.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/classes.R R/helper_functions.R R/main_functions.R R/methods.R
build
build/vignette.rds
data
data/exomecounts.rda
inst
inst/doc
inst/doc/exomeCopy.R
inst/doc/exomeCopy.Rnw
inst/doc/exomeCopy.pdf
inst/extdata
inst/extdata/1000Genomes_files.txt
inst/extdata/mapping.bam
inst/extdata/mapping.bam.bai
inst/extdata/mapping.sam
inst/extdata/reference.fa
inst/extdata/reference.fa.fai
inst/extdata/targets.bed
man
man/ExomeCopy-class.Rd man/compileCopyCountSegments.Rd man/copyCountSegments.Rd man/countBamInGRanges.Rd man/exomeCopy-package.Rd man/exomeCopy.Rd man/exomecounts.Rd man/generateBackground.Rd man/getGCcontent.Rd man/negLogLike.Rd man/plot.exomeCopyObject.Rd man/plotCompiledCNV.Rd man/subdivideGRanges.Rd
src
src/exomeCopy.c
vignettes
vignettes/exomeCopy.Rnw
vignettes/exomeCopy.bib

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