NGScopy: NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing
Version 1.10.0

NGScopy provides a quantitative caller for detecting copy number variations in next generation sequencing (NGS), including whole genome sequencing (WGS), whole exome sequencing (WES) and targeted panel sequencing (TPS). The caller can be parallelized by chromosomes to use multiple processors/cores on one computer.

Browse man pages Browse package API and functions Browse package files

AuthorXiaobei Zhao [aut, cre, cph]
Bioconductor views CopyNumberVariation DNASeq ExomeSeq Sequencing TargetedResequencing WholeGenome
Date of publicationNone
MaintainerXiaobei Zhao <xiaobei@binf.ku.dk>
LicenseGPL (>=2)
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("NGScopy")

Man pages

df.to.gr: Convert a data.frame to a GRanges object
help_segmtype: Get help for segmentation functions
NGScopy-class: Detection of copy number variations in next generation...
ngscopy_cmdline_example: Run an example of NGScopy at UNIX-like command line
NGScopy-package: NGScopy: Detection of copy number variations in next...
ngscopy_unittest: A wrapper to run unit testing of NGScopy
parse_segmtype: Parse the type of segmentation
read_regions: Read regions from a data.frame, a file or a connection.

Functions

NGScopy Man page
NGScopy-class Man page
NGScopy-package Man page
bound_end Source code
calc_cn Source code
calc_segm Source code
check.packages Source code
check_regions Source code
check_segmtype Source code
count_starts Source code
df.to.gr Man page Source code
help_segmtype Man page Source code Source code
make_windows Source code
ngscopy_cmdline_example Man page Source code
ngscopy_unittest Man page Source code
parse_mfrow Source code
parse_ref Source code
parse_scales Source code
parse_segmfunc Source code
parse_segmtype Man page Source code Source code
plot_out Source code
proc_segm Source code
read_regions Man page Source code
ref_to_refid Source code
ref_to_reflength Source code
ref_to_reflength2 Source code
ref_to_refname Source code
ref_to_regions Source code
refid_to_refname Source code
refname_to_refid Source code
sort_regions Source code
trim_regions Source code
unit_plot_out Source code
unit_plot_segm Source code
vconcat Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/NGScopy-package.R
R/archive.R
R/interface-to-cran-changepoint.R
R/ngscopy-internal.R
R/ngscopy-test.R
R/ngscopy.R
build
build/vignette.rds
inst
inst/CITATION
inst/bin
inst/bin/ngscopy
inst/doc
inst/doc/NGScopy-vignette.R
inst/doc/NGScopy-vignette.Rnw
inst/doc/NGScopy-vignette.pdf
inst/extdata
inst/extdata/hg19_chr6_0_171115067.txt
inst/tests
inst/tests/ngscopy_unittest.R
man
man/NGScopy-class.Rd
man/NGScopy-package.Rd
man/df.to.gr.Rd
man/help_segmtype.Rd
man/ngscopy_cmdline_example.Rd
man/ngscopy_unittest.Rd
man/parse_segmtype.Rd
man/read_regions.Rd
vignettes
vignettes/NGScopy-vignette.Rnw
vignettes/NGScopy-vignette.bib
vignettes/Xvignette.sty
vignettes/bioinfo.sty
vignettes/ngscopy-case0
vignettes/ngscopy-case0/27_N8
vignettes/ngscopy-case0/27_N8/ngscopy_out.pdf
vignettes/ngscopy-case0/90_N8
vignettes/ngscopy-case0/90_N8/ngscopy_out.pdf
vignettes/ngscopy-case1.R
vignettes/ngscopy-case1b
vignettes/ngscopy-case1b-cmdline.out
vignettes/ngscopy-case1b-cmdline.sh
vignettes/ngscopy-case1b/ngscopy_out.pdf
vignettes/ngscopy-case1c
vignettes/ngscopy-case1c/ngscopy_out.pdf
vignettes/ngscopy-case2.R
vignettes/ngscopy-case2b
vignettes/ngscopy-case2b/27_N8
vignettes/ngscopy-case2b/27_N8/ngscopy_out.pdf
vignettes/ngscopy-case2b/90_N8
vignettes/ngscopy-case2b/90_N8/ngscopy_out.pdf
vignettes/ngscopy.x
NGScopy documentation built on May 20, 2017, 9:31 p.m.