.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
Jenkinsfile
LICENSE.txt
NAMESPACE
R/analysis.R
R/globals.R
R/import.R
R/io.R
R/reporting.R
README.Rmd
README.md
docs/articles/build_metrics.Rmd
docs/articles/build_metrics.html
docs/articles/build_metrics_files/figure-html/unnamed-chunk-11-1.png
docs/articles/build_metrics_files/figure-html/unnamed-chunk-4-1.png
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docs/articles/extracting_metrics.html
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docs/articles/extracting_metrics_files/figure-html/unnamed-chunk-6-1.png
docs/articles/extracting_metrics_files/figure-html/unnamed-chunk-9-1.png
docs/articles/index.html
docs/articles/intro.html
docs/articles/intro_files/figure-html/unnamed-chunk-6-1.png
docs/articles/intro_files/figure-html/unnamed-chunk-7-1.png
docs/articles/pcrfree_vs_nano.csv
docs/articles/pcrfree_vs_nano.subset.csv
docs/articles/quick_start.html
docs/articles/quick_start_files/figure-html/unnamed-chunk-7-1.png
docs/articles/quick_start_files/figure-html/unnamed-chunk-8-1.png
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docs/articles/r5.params_1.csv
docs/articles/simulations.html
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docs/articles/stratified_counts.html
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docs/articles/stratified_counts_files/figure-html/unnamed-chunk-8-1.png
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docs/authors.html
docs/examples/README-unnamed-chunk-5-1.png
docs/examples/README-unnamed-chunk-6-1.png
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/reference/compare_hdi.html
docs/reference/estimate_hdi.html
docs/reference/extract.html
docs/reference/extract_metrics.html
docs/reference/happyCompare_list.html
docs/reference/hc_plot_hdi.html
docs/reference/hc_plot_roc.html
docs/reference/hc_summarise_metrics.html
docs/reference/index.html
docs/reference/is_haplocompare.html
docs/reference/is_happy_summary.html
docs/reference/plot.html
docs/reference/print.haplocompare.html
docs/reference/print.happy_summary.html
docs/reference/read_samplesheet.html
docs/reference/read_samplesheet_.html
docs/reference/summary.happy_summary.html
docs/reference/tabulate.html
docs/reference/tidy.happy_summary.html
docs/reference/tidy.html
happyCompare.Rproj
inst/Rscript/simulate_data.R
man/compare_hdi.Rd
man/estimate_hdi.Rd
man/extract_metrics.Rd
man/hc_plot_hdi.Rd
man/hc_plot_roc.Rd
man/hc_summarise_metrics.Rd
man/read_samplesheet.Rd
man/read_samplesheet_.Rd
tests/data/pcrfree_vs_nano/build_metrics/NA12878-I30_S1.summary.csv
tests/data/pcrfree_vs_nano/build_metrics/NA12878-I33_S1.summary.csv
tests/data/pcrfree_vs_nano/build_metrics/NA12878-R1_S1.summary.csv
tests/data/pcrfree_vs_nano/build_metrics/NA12878-R2_S1.summary.csv
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tests/data/pcrfree_vs_nano/filtered_happy/NA12878-I30_S1.roc.Locations.INDEL.csv.gz
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tests/data/pcrfree_vs_nano/filtered_happy/NA12878-I33_S1.roc.all.csv.gz
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-I33_S1.summary.csv
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R1_S1.extended.csv
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R1_S1.roc.Locations.INDEL.PASS.csv.gz
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R1_S1.roc.Locations.INDEL.SEL.csv.gz
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R1_S1.roc.Locations.INDEL.csv.gz
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R1_S1.roc.all.csv.gz
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R1_S1.summary.csv
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R2_S1.extended.csv
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R2_S1.roc.Locations.INDEL.PASS.csv.gz
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R2_S1.roc.Locations.INDEL.SEL.csv.gz
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R2_S1.roc.Locations.INDEL.csv.gz
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R2_S1.roc.all.csv.gz
tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R2_S1.summary.csv
tests/testthat.R
tests/testthat/pcrfree_vs_nano.tests.csv
tests/testthat/test.hc_plot_hdi.pdf
tests/testthat/test.hc_plot_roc.pdf
tests/testthat/test_analysis.R
tests/testthat/test_io.R
tests/testthat/test_reporting.R
vignettes/extracting_metrics.Rmd
vignettes/generate_rds.R
vignettes/pcrfree_vs_nano.Rds
vignettes/pcrfree_vs_nano.csv
vignettes/pcrfree_vs_nano.subset.Rds
vignettes/pcrfree_vs_nano.subset.csv
vignettes/quick_start.Rmd
vignettes/r5.params_1.csv
vignettes/simulations.Rmd
vignettes/stratified_counts.Rds
vignettes/stratified_counts.Rmd