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

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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.

Author
Xiaobei Zhao [aut, cre, cph]
Date of publication
None
Maintainer
Xiaobei Zhao <xiaobei@binf.ku.dk>
License
GPL (>=2)
Version
1.8.0

View on Bioconductor

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.

Files in this package

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