├── R └── RCNV_seq-helper.R ├── README.md ├── image ├── cn.mops-segplot.png ├── cna-norm.png ├── cnv-countOverlaps.png ├── cnv-seq-plot.png ├── count2.png ├── normalised-count2.png ├── plotBias.png ├── plotCorrection.png ├── plotDefaultSegments.png ├── plotSegment_case1.png └── plotSegment_case2.png ├── inst └── script │ ├── CNAnorm.R │ ├── CNV-seq.R │ ├── HMMcopy.R │ ├── RCNV_seq.R │ ├── TitanCNA-helper.R │ ├── TitanCNA.R │ ├── cn.mops.R │ ├── countOverlaps.R │ ├── seqCNA.R │ └── testCounts.R ├── result files ├── countOverlapresult.tsv ├── tumor.hits-vs-normal.hits.window-10000.minw-4.cnv └── tumor.hits-vs-normal.hits.window-10000.minw-4.count └── vignettes └── seqCNA.Rnw /R/RCNV_seq-helper.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/R/RCNV_seq-helper.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/README.md -------------------------------------------------------------------------------- /image/cn.mops-segplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/cn.mops-segplot.png -------------------------------------------------------------------------------- /image/cna-norm.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/cna-norm.png -------------------------------------------------------------------------------- /image/cnv-countOverlaps.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/cnv-countOverlaps.png -------------------------------------------------------------------------------- /image/cnv-seq-plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/cnv-seq-plot.png -------------------------------------------------------------------------------- /image/count2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/count2.png -------------------------------------------------------------------------------- /image/normalised-count2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/normalised-count2.png -------------------------------------------------------------------------------- /image/plotBias.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/plotBias.png -------------------------------------------------------------------------------- /image/plotCorrection.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/plotCorrection.png -------------------------------------------------------------------------------- /image/plotDefaultSegments.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/plotDefaultSegments.png -------------------------------------------------------------------------------- /image/plotSegment_case1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/plotSegment_case1.png -------------------------------------------------------------------------------- /image/plotSegment_case2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/image/plotSegment_case2.png -------------------------------------------------------------------------------- /inst/script/CNAnorm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/inst/script/CNAnorm.R -------------------------------------------------------------------------------- /inst/script/CNV-seq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/inst/script/CNV-seq.R -------------------------------------------------------------------------------- /inst/script/HMMcopy.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/inst/script/HMMcopy.R -------------------------------------------------------------------------------- /inst/script/RCNV_seq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/inst/script/RCNV_seq.R -------------------------------------------------------------------------------- /inst/script/TitanCNA-helper.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/inst/script/TitanCNA-helper.R -------------------------------------------------------------------------------- /inst/script/TitanCNA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/inst/script/TitanCNA.R -------------------------------------------------------------------------------- /inst/script/cn.mops.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/inst/script/cn.mops.R -------------------------------------------------------------------------------- /inst/script/countOverlaps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/inst/script/countOverlaps.R -------------------------------------------------------------------------------- /inst/script/seqCNA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/inst/script/seqCNA.R -------------------------------------------------------------------------------- /inst/script/testCounts.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/inst/script/testCounts.R -------------------------------------------------------------------------------- /result files/countOverlapresult.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/result files/countOverlapresult.tsv -------------------------------------------------------------------------------- /result files/tumor.hits-vs-normal.hits.window-10000.minw-4.cnv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/result files/tumor.hits-vs-normal.hits.window-10000.minw-4.cnv -------------------------------------------------------------------------------- /result files/tumor.hits-vs-normal.hits.window-10000.minw-4.count: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/result files/tumor.hits-vs-normal.hits.window-10000.minw-4.count -------------------------------------------------------------------------------- /vignettes/seqCNA.Rnw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/copy-number-analysis/HEAD/vignettes/seqCNA.Rnw --------------------------------------------------------------------------------