Files in jhrcook/KrasAlleleCna
The Allele-Specific CNA Analysis of KRAS in CRC
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/data.R
R/download-data.R
R/heatmap_genotype.R
R/parse_vcf.R
R/tidy_annovar.R
R/utilities.R
README.Rmd
README.md
_pkgdown.yml
appveyor.yml
bash-scripts/download_process_tcga_bams.sh
codecov.yml
data/allele_data_filt.rda
data/allele_depth_tib.rda
data/annovar_tib.rda
data/cnv_tib.rda
data/tidy_tcga_sample_sheet.rda
docs/LICENSE.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/a01-download-getgdcdata.html
docs/articles/b01-dataprep-processannovar.html
docs/articles/b01-dataprep-processannovar_files/kePrint-0.0.1/kePrint.js
docs/articles/b02-dataprep-processmpileup.html
docs/articles/b02-dataprep-processmpileup_files/kePrint-0.0.1/kePrint.js
docs/articles/c01-calccopynum.html
docs/articles/d01-plotresults.html
docs/articles/d01-plotresults_files/figure-html/genotypeheatmap-1.png
docs/articles/d01-plotresults_files/figure-html/genotypeheatmap-2.png
docs/articles/d01-plotresults_files/figure-html/lateralplot-1.png
docs/articles/d01-plotresults_files/figure-html/plot1-1.png
docs/articles/download-data.html
docs/articles/index.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/allele_data_filt.html
docs/reference/allele_depth_tib.html
docs/reference/annovar_tib.html
docs/reference/choose_one_filename.html
docs/reference/cnv_tib.html
docs/reference/failed_downloads.html
docs/reference/figures/README-genotypeheatmap-1.png
docs/reference/figures/README-genotypeheatmap-2.png
docs/reference/figures/README-lateralplot-1.png
docs/reference/figures/logo.png
docs/reference/figures/logo_OLD.png
docs/reference/index.html
docs/reference/n_unique.html
docs/reference/parse_annovar_mutation.html
docs/reference/parse_vcf.html
docs/reference/plot_genotype_heatmap.html
docs/reference/tcga_manifest.html
docs/reference/tcga_sample_sheet.html
docs/reference/tidy_tcga_sample_sheet.html
docs/reference/two_filename_handler.html
inst/WORDLIST
inst/extdata/annovar_output_list.rds
inst/extdata/failed_downloads.txt
inst/extdata/mpileup_output_list.rds
inst/extdata/tcga_copynumber.tsv.gz
inst/extdata/tcga_filename_list.txt
inst/extdata/tcga_manifest.tsv
inst/extdata/tcga_purity_ploidy.tsv
inst/extdata/tcga_sample_sheet.tsv
man/allele_data_filt.Rd
man/allele_depth_tib.Rd
man/annovar_tib.Rd
man/choose_one_filename.Rd
man/cnv_tib.Rd
man/figures/README-genotypeheatmap-1.png
man/figures/README-genotypeheatmap-2.png
man/figures/README-lateralplot-1.png
man/figures/logo.png
man/figures/logo_OLD.png
man/n_unique.Rd
man/parse_annovar_mutation.Rd
man/parse_vcf.Rd
man/plot_genotype_heatmap.Rd
man/tidy_tcga_sample_sheet.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/spelling.R
tests/testthat.R
tests/testthat/005ea64b-18e7-4f50-b940-38322a96e034_mpileup.vcf
tests/testthat/test-download-createfilenamelists.R
tests/testthat/test-heatmap_genotype.R
tests/testthat/test-parse_vcf.R
tests/testthat/test-tidy-annovar.R
tests/testthat/test-utilities.R
tests/testthat/test_annovar_tibbles.rds
vignettes/.gitignore
vignettes/a01-download-getgdcdata.Rmd
vignettes/b01-dataprep-processannovar.Rmd
vignettes/b02-dataprep-processmpileup.Rmd
vignettes/c01-calccopynum.Rmd
vignettes/d01-plotresults.Rmd
vignettes/d01-plotresults_cache/html/__packages
vignettes/d01-plotresults_cache/html/genotypeheatmap_6562194cc759a9415b528c21539d54d4.RData
vignettes/d01-plotresults_cache/html/genotypeheatmap_6562194cc759a9415b528c21539d54d4.rdb
vignettes/d01-plotresults_cache/html/genotypeheatmap_6562194cc759a9415b528c21539d54d4.rdx
