Files in shahcompbio/signals
Single Cell Genomes with Allele Specificity
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/docker.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
ASCN-RNA.Rmd
DESCRIPTION
Dockerfile
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/.gitignore
R/RcppExports.R
R/callASCN.R
R/callHSCN.R
R/callHSCNrna.R
R/clustering.R
R/col_palettes.R
R/combinedata.R
R/combinedata_rna.R
R/convert.R
R/heatmap_plot.R
R/heatmap_plot_rna.R
R/import_packages.R
R/missegregations.R
R/plotting.R
R/plotting_rna.R
R/print.methods.R
R/signals-package.R
R/sim-data.R
R/sysdata.rda
R/util.R
R/utils-pipe.R
R/viterbi.R
README.md
_pkgdown.yml
codecov.yml
data/CNbins.rda
data/CNmetrics.rda
data/SNV.rda
data/countsmatrix.rda
data/cytoband_map.rda
data/dlpbins.rda
data/fragile_sites.rda
data/fragile_sites_location.rda
data/gene_locations.rda
data/haplotypes.rda
data/haplotypes_rna.rda
data/hg19_chrlength.rda
data/hg19chrom_coordinates.rda
docs/articles/ASCN_files/figure-html/unnamed-chunk-10-1.png
docs/articles/ASCN_files/figure-html/unnamed-chunk-11-1.png
docs/articles/ASCN_files/figure-html/unnamed-chunk-12-1.png
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docs/articles/ASCN_files/figure-html/unnamed-chunk-8-1.png
docs/articles/ASCN_files/figure-html/unnamed-chunk-9-1.png
docs/articles/BetaBinom_files/figure-html/unnamed-chunk-3-1.png
docs/articles/BetaBinom_files/figure-html/unnamed-chunk-4-1.png
docs/articles/BetaBinom_files/figure-html/unnamed-chunk-5-1.png
docs/articles/karyoplot_files/figure-html/unnamed-chunk-4-1.png
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docs/articles/karyoplot_files/figure-html/unnamed-chunk-6-1.png
docs/articles/karyoplot_files/figure-html/unnamed-chunk-7-1.png
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
man/add_gene_locations_to_seurat.Rd
man/callAlleleSpecificCN.Rd
man/callAlleleSpecificCNfromHSCN.Rd
man/callHaplotypeSpecificCN.Rd
man/coord_to_arm.Rd
man/getBins.Rd
man/pipe.Rd
man/plotBAFperstate.Rd
man/plotCNprofile.Rd
man/plotCNprofileBAF.Rd
man/plotHeatmap.Rd
man/plot_clusters_used_for_phasing.Rd
man/rephasebins.Rd
man/scale_color_scCN.Rd
man/scale_fill_scCN.Rd
man/umap_clustering.Rd
policy.xml
src/.gitignore
src/RcppExports.cpp
src/code.cpp
tests/testthat.R
tests/testthat/test-ascn.R
tests/testthat/test-clustering.R
tests/testthat/test-complexphasing.R
tests/testthat/test-heatmapanno.R
tests/testthat/test-hscn.R
tests/testthat/test-masking.R
tests/testthat/test-tests.R
tests/testthat/test-util.R
vignettes/.gitignore
vignettes/ASCN-RNA.Rmd
vignettes/ASCN.Rmd
vignettes/BetaBinom.Rmd
vignettes/basic_scdnaseq.Rmd
