saasCNV: Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

Perform joint segmentation on two signal dimensions derived from total read depth (intensity) and allele specific read depth (intensity) for whole genome sequencing (WGS), whole exome sequencing (WES) and SNP array data.

AuthorZhongyang Zhang [aut, cre], Ke Hao [aut], Nancy R. Zhang [ctb]
Date of publication2016-05-18 02:04:56
MaintainerZhongyang Zhang <zhongyang.zhang@mssm.edu>
LicenseGPL (>= 2)
Version0.3.4
https://zhangz05.u.hpc.mssm.edu/saasCNV/

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Files in this package

saasCNV
saasCNV/inst
saasCNV/inst/doc
saasCNV/inst/doc/saasCNV.pdf
saasCNV/NAMESPACE
saasCNV/data
saasCNV/data/snp.segs.RData
saasCNV/data/snp.segs.merge.RData
saasCNV/data/snp.cnv.refine.anno.RData
saasCNV/data/seq.segs.merge.RData
saasCNV/data/seq.segs.RData
saasCNV/data/snp.cnv.anno.RData
saasCNV/data/seq.data.RData
saasCNV/data/snp.cnv.RData
saasCNV/data/snp.cnv.refine.RData
saasCNV/data/seq.cnv.RData
saasCNV/R
saasCNV/R/seg.summary.R saasCNV/R/cnv.data.chr.R saasCNV/R/BAF2mBAF.R saasCNV/R/delta.sd.R saasCNV/R/diagnosis.QQ.plot.R saasCNV/R/msscan_tools.R saasCNV/R/genome.wide.plot.R saasCNV/R/check.overlap.R saasCNV/R/vcf2txt.R saasCNV/R/impute.missing.data.R saasCNV/R/cnv.call.R saasCNV/R/joint.segmentation.R saasCNV/R/merging.segments.R saasCNV/R/reannotate.CNV.res.R saasCNV/R/compute.baseline.manual.R saasCNV/R/compute.baseline.R saasCNV/R/merging.segments.chr.R saasCNV/R/diagnosis.cluster.plot.R saasCNV/R/snp.refine.boundary.R saasCNV/R/snp.cnv.data.R saasCNV/R/GC.adjust.R saasCNV/R/NGS.CNV.R saasCNV/R/Mode.R saasCNV/R/cnv.data.R saasCNV/R/diagnosis.seg.plot.chr.R saasCNV/R/SNP.CNV.R
saasCNV/MD5
saasCNV/DESCRIPTION
saasCNV/ChangeLog
saasCNV/man
saasCNV/man/NGS.CNV.Rd saasCNV/man/GC.adjust.Rd saasCNV/man/merging.segments.Rd saasCNV/man/joint.segmentation.Rd saasCNV/man/snp.refine.boundary.Rd saasCNV/man/cnv.data.Rd saasCNV/man/vcf2txt.Rd saasCNV/man/cnv.call.Rd saasCNV/man/SNP.CNV.Rd saasCNV/man/saasCNV-package.Rd saasCNV/man/internals.Rd saasCNV/man/genome.wide.plot.Rd saasCNV/man/snp.cnv.data.Rd saasCNV/man/diagnosis.seg.plot.chr.Rd saasCNV/man/diagnosis.cluster.plot.Rd saasCNV/man/reannotate.CNV.res.Rd

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