Files in zhouzilu/iCNV
Integrated Copy Number Variation detection
.gitattributes
DESCRIPTION
NAMESPACE
R/bambaf_from_vcf.R
R/bed_generator.R
R/get_array_input.R
R/iCNV_detection_function.R
R/icnv_output_to_gb.R
R/output_list_function.R
R/plotHMMscore_function.R
R/plot_intensity.R
R/plotindi_function.R
README.md
data/icnv.demo.array_lrrbaf_22.rda
data/icnv.demo.bambaf_22.rda
data/icnv.demo.plrObj_22.rda
data/icnv.demo.plrObj_22_2.rda
data/icnv_res0.rda
inst/NEWS
inst/doc/iCNV-vignette.html
inst/doc/iCNV-vignette.pdf
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-1-1.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-10-1.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-10-2.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-10-3.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-11-1.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-12-1.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-12-2.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-13-1.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-14-1.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-14-2.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-4-1.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-6-1.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-8-1.png
inst/doc/iCNV-vignette_files/figure-html/unnamed-chunk-9-1.png
inst/extdata/NA06994.csv.arrayicnv
inst/extdata/NA06994.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA10847.csv.arrayicnv
inst/extdata/NA10847.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA11840.csv.arrayicnv
inst/extdata/NA11840.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA12249.csv.arrayicnv
inst/extdata/NA12249.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA12716.csv.arrayicnv
inst/extdata/NA12716.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA12750.csv.arrayicnv
inst/extdata/NA12750.mapped.ILLUMINA.bwa.CEU.exome.20130415.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA12751.csv.arrayicnv
inst/extdata/NA12751.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA12760.csv.arrayicnv
inst/extdata/NA12760.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA12761.csv.arrayicnv
inst/extdata/NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA12763.csv.arrayicnv
inst/extdata/NA12763.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18966.csv.arrayicnv
inst/extdata/NA18966.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18967.csv.arrayicnv
inst/extdata/NA18967.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18968.csv.arrayicnv
inst/extdata/NA18968.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18969.csv.arrayicnv
inst/extdata/NA18969.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18970.csv.arrayicnv
inst/extdata/NA18970.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18971.csv.arrayicnv
inst/extdata/NA18971.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18972.csv.arrayicnv
inst/extdata/NA18972.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18973.csv.arrayicnv
inst/extdata/NA18973.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18974.csv.arrayicnv
inst/extdata/NA18974.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18975.csv.arrayicnv
inst/extdata/NA18975.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18976.csv.arrayicnv
inst/extdata/NA18976.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18981.csv.arrayicnv
inst/extdata/NA18981.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18987.csv.arrayicnv
inst/extdata/NA18987.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18990.csv.arrayicnv
inst/extdata/NA18990.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA18991.csv.arrayicnv
inst/extdata/NA18991.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19098.csv.arrayicnv
inst/extdata/NA19098.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19119.csv.arrayicnv
inst/extdata/NA19119.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19131.csv.arrayicnv
inst/extdata/NA19131.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19137.csv.arrayicnv
inst/extdata/NA19137.mapped.ILLUMINA.bwa.YRI.exome.20130415.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19138.csv.arrayicnv
inst/extdata/NA19138.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19141.csv.arrayicnv
inst/extdata/NA19141.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19143.csv.arrayicnv
inst/extdata/NA19143.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19144.csv.arrayicnv
inst/extdata/NA19144.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19152.csv.arrayicnv
inst/extdata/NA19152.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19153.csv.arrayicnv
inst/extdata/NA19153.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19159.csv.arrayicnv
inst/extdata/NA19159.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19160.csv.arrayicnv
inst/extdata/NA19160.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19171.csv.arrayicnv
inst/extdata/NA19171.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19200.csv.arrayicnv
inst/extdata/NA19200.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19201.csv.arrayicnv
inst/extdata/NA19201.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19204.csv.arrayicnv
inst/extdata/NA19204.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19206.csv.arrayicnv
inst/extdata/NA19206.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19207.csv.arrayicnv
inst/extdata/NA19207.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19209.csv.arrayicnv
inst/extdata/NA19209.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19210.csv.arrayicnv
inst/extdata/NA19210.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/NA19223.csv.arrayicnv
inst/extdata/NA19223.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam.chr22.sorted.bam.vcf.gz.filter
inst/extdata/bam_vcf.list
man/bambaf_from_vcf.Rd
man/bed_generator.Rd
man/chr.Rd
man/filenm.Rd
man/get_array_input.Rd
man/iCNV_detection.Rd
man/icnv_output_to_gb.Rd
man/icnv_res0.Rd
man/ngs_baf.Rd
man/ngs_baf.chr.Rd
man/ngs_baf.id.Rd
man/ngs_baf.nm.Rd
man/ngs_baf.pos.Rd
man/ngs_plr.Rd
man/ngs_plr.pos.Rd
man/normObj.Rd
man/output_list.Rd
man/plotHMMscore.Rd
man/plot_intensity.Rd
man/plotindi.Rd
man/projname.Rd
man/qcObj.Rd
man/sampname.Rd
man/sampname_qc.Rd
man/snp_baf.Rd
man/snp_baf.pos.Rd
man/snp_lrr.Rd
man/snp_lrr.pos.Rd
vignettes/iCNV-vignette.Rmd
vignettes/iCNV-vignette.html
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