Files in whtns/varbintools
Sequence Based Copy Number Detection Using Variable Bin Lengths
.Rbuildignore
.Rhistory
.gitignore
DESCRIPTION
NAMESPACE
R/CNProcessingCentromeres_GC_Mergelevels_correction_RG.R
R/CN_Seg_GC_filter_correctionRG.R
R/Mergelevels.R
R/bin_median_filter.R
R/filterGC.R
R/formatting.R
R/gene_anno.R
R/heatmap.R
R/phenograph.R
R/plotting.R
R/render_dashboard.R
R/segment_varbin.R
R/umap.R
R/utils-pipe.R
README.md
_pkgdown.yml
data/bins_in_cna_pipeline.rda
data/cosmic_census.rda
data/mdamb231_bin.rda
data/mdamb231_dbf.rda
data/mdamb231_ratio.rda
data/mdamb231_seg.rda
docs/404.html
docs/articles/images/F1.large.jpg
docs/articles/index.html
docs/articles/varbintools.html
docs/articles/varbintools_files/crosstalk-1.0.0/css/crosstalk.css
docs/articles/varbintools_files/crosstalk-1.0.0/js/crosstalk.js
docs/articles/varbintools_files/crosstalk-1.0.0/js/crosstalk.js.map
docs/articles/varbintools_files/crosstalk-1.0.0/js/crosstalk.min.js
docs/articles/varbintools_files/crosstalk-1.0.0/js/crosstalk.min.js.map
docs/articles/varbintools_files/datatables-binding-0.9/datatables.js
docs/articles/varbintools_files/datatables-css-0.0.0/datatables-crosstalk.css
docs/articles/varbintools_files/dt-core-1.10.19/css/jquery.dataTables.extra.css
docs/articles/varbintools_files/dt-core-1.10.19/css/jquery.dataTables.min.css
docs/articles/varbintools_files/dt-core-1.10.19/js/jquery.dataTables.min.js
docs/articles/varbintools_files/figure-html/bin_plot-1.png
docs/articles/varbintools_files/figure-html/bin_plot-2.png
docs/articles/varbintools_files/figure-html/consensus-1.png
docs/articles/varbintools_files/figure-html/consensus_heatmap_annotates-1.png
docs/articles/varbintools_files/figure-html/making_heatmap-1.png
docs/articles/varbintools_files/figure-html/nj_tree-1.png
docs/articles/varbintools_files/figure-html/segmentation-1.png
docs/articles/varbintools_files/figure-html/umap_with_cl-1.png
docs/articles/varbintools_files/figure-html/unnamed-chunk-2-1.png
docs/articles/varbintools_files/figure-html/unnamed-chunk-5-1.png
docs/articles/varbintools_files/figure-html/unnamed-chunk-7-1.png
docs/articles/varbintools_files/figure-html/unnamed-chunk-8-1.png
docs/articles/varbintools_files/figure-html/unnamed-chunk-9-1.png
docs/articles/varbintools_files/htmlwidgets-1.3/htmlwidgets.js
docs/articles/varbintools_files/jquery-1.12.4/LICENSE.txt
docs/articles/varbintools_files/jquery-1.12.4/jquery.min.js
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/CNProcessingCentromeres.html
docs/reference/CN_Seg_GC_filter_correctionRG.html
docs/reference/MergeLevels.html
docs/reference/bin_median_filter.html
docs/reference/breakpoint_filter.html
docs/reference/combine.func.html
docs/reference/create_chr_bar.html
docs/reference/filter_vb_file.html
docs/reference/format_chr_for_plot.html
docs/reference/format_ggaes.html
docs/reference/gene_anno.html
docs/reference/index.html
docs/reference/lowess.gc.html
docs/reference/pipe.html
docs/reference/plot_bin.html
docs/reference/plot_loess_segments.html
docs/reference/plot_merged_segments.html
docs/reference/pretty_ratio_plot.html
docs/reference/ratio_plot.html
docs/reference/render_varbin_dashboard.html
docs/reference/segment_varbin.html
docs/reference/varbin_complexheatmap.html
docs/reference/varbin_consensus_complexheatmap.html
docs/reference/varbin_heatmap.3.html
docs/reference/varbin_heatmap.html
docs/reference/varbin_pheno.html
docs/reference/varbin_umap.html
inst/bin/All_raw_bin_metrics.pl
inst/bin/All_stat_metrics.pl
inst/bin/All_stat_metrics_summary.pl
inst/bin/run_bowtie2_varbin.pl
inst/bin/run_bowtie2_varbin_nextseq.pl
inst/bin/varbin.sam.2.py
inst/extdata/cells_fastq/blvb/ES16-54_SKBR3P11C2P1-C37_S1957_L005_R1_001-bl.vb
inst/extdata/cells_fastq/vbdir/ES16-54_SKBR3P11C2P1-C37_S1957_L005_R1_001.vb
inst/extdata/lib/._cancer_gene_census.csv
inst/extdata/lib/100kb_excluded.txt
inst/extdata/lib/10M_with_a_chr6_region.excluded.txt
inst/extdata/lib/1M_with_a_chr6_region.excluded.txt
inst/extdata/lib/200kb_with_a_chr6_region.excluded.txt
inst/extdata/lib/2M_with_a_chr6_region.excluded.txt
inst/extdata/lib/300kb_excluded.txt
inst/extdata/lib/400kb_excluded.txt
inst/extdata/lib/500kb_excluded.txt
inst/extdata/lib/5M_with_a_chr6_region.excluded.txt
inst/extdata/lib/CNA.config
inst/extdata/lib/bin.boundaries.100k.bowtie.k50.sorted.bin_not_removed.txt
inst/extdata/lib/bin.boundaries.10M.bowtie.k50.sorted.bin_not_removed.txt
inst/extdata/lib/bin.boundaries.1M.bowtie.k50.sorted.bin_not_removed.txt
inst/extdata/lib/bin.boundaries.200k.bowtie.sorted.bin.txt
inst/extdata/lib/bin.boundaries.2M.bowtie.k50.sorted.bin_not_removed.txt
inst/extdata/lib/bin.boundaries.300k.bowtie.k50.sorted.bin_not_removed_MH.txt
inst/extdata/lib/bin.boundaries.400k.bowtie.k50.sorted.bin_not_removed.txt
inst/extdata/lib/bin.boundaries.500k.bowtie.k50.sorted.bin_not_removed.txt
inst/extdata/lib/bin.boundaries.5M.bowtie.k50.sorted.bin_not_removed.txt
inst/extdata/lib/bins_in_cna_pipeline_bands.txt
inst/extdata/lib/cancer_gene_census.csv
inst/extdata/lib/hg19.chromInfo.cumsum.txt
inst/extdata/lib/varbin.gc.content.100k.bowtie.k50.hg19.bin_not_removed.txt
inst/extdata/lib/varbin.gc.content.10M.bowtie.k50.hg19.bin_not_removed.txt
inst/extdata/lib/varbin.gc.content.1M.bowtie.k50.hg19.bin_not_removed.txt
inst/extdata/lib/varbin.gc.content.200k.bowtie.k50.hg19.bin_not_removed.txt
inst/extdata/lib/varbin.gc.content.2M.bowtie.k50.hg19.bin_not_removed.txt
inst/extdata/lib/varbin.gc.content.300k.bowtie.k50.hg19.bin_not_removed_MH.txt
inst/extdata/lib/varbin.gc.content.400k.bowtie.k50.hg19.bin_not_removed.txt
inst/extdata/lib/varbin.gc.content.500k.bowtie.k50.hg19.bin_not_removed.txt
inst/extdata/lib/varbin.gc.content.5M.bowtie.k50.hg19.bin_not_removed.txt
man/CNProcessingCentromeres.Rd
man/CN_Seg_GC_filter_correctionRG.Rd
man/MergeLevels.Rd
man/bin_median_filter.Rd
man/breakpoint_filter.Rd
man/combine.func.Rd
man/create_chr_bar.Rd
man/filter_vb_file.Rd
man/format_chr_for_plot.Rd
man/format_ggaes.Rd
man/gene_anno.Rd
man/lowess.gc.Rd
man/pipe.Rd
man/plot_bin.Rd
man/plot_loess_segments.Rd
man/plot_merged_segments.Rd
man/pretty_ratio_plot.Rd
man/ratio_plot.Rd
man/render_varbin_dashboard.Rd
man/segment_varbin.Rd
man/varbin_complexheatmap.Rd
man/varbin_consensus_complexheatmap.Rd
man/varbin_heatmap.3.Rd
man/varbin_heatmap.Rd
man/varbin_pheno.Rd
man/varbin_umap.Rd
varbintools.Rproj
vignettes/.Rhistory
vignettes/.gitignore
vignettes/images/._F1.large.jpg
vignettes/images/F1.large.jpg
vignettes/varbintools.Rmd
