Files in alkodsi/ctDNAtools
Analyze Circulating Tumor DNA Sequencing Data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/analyze_fragmentation.R
R/bin_fragment_size.R
R/create_background_panel.R
R/create_background_panel_instance.R
R/create_black_list.R
R/data.R
R/extract_trinucleotide_context.R
R/filter_mutations.R
R/get_background_rate.R
R/get_bam_SM.R
R/get_bam_chr.R
R/get_fragment_size.R
R/get_hist_bins.R
R/get_mutation_read_names.R
R/get_mutations_fragment_size.R
R/get_mutations_read_counts.R
R/get_mutations_read_names.R
R/get_read_counts.R
R/merge_mutations_in_phase.R
R/positivity_test.R
R/simulator.R
R/summarize_fragment_size.R
R/test_ctDNA.R
R/vcf_to_mutations_df.R
R/verify_tag.R
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
data/mutations.rda
data/targets.rda
inst/CITATION
inst/extdata/N1.bai
inst/extdata/N1.bam
inst/extdata/N2.bai
inst/extdata/N2.bam
inst/extdata/N3.bai
inst/extdata/N3.bam
inst/extdata/T1.bai
inst/extdata/T1.bam
inst/extdata/T2.bai
inst/extdata/T2.bam
man/analyze_fragmentation.Rd
man/bin_fragment_size.Rd
man/compare_simulated_observed.Rd
man/create_background_panel.Rd
man/create_background_panel_instance.Rd
man/create_black_list.Rd
man/extract_trinucleotide_context.Rd
man/figures/ctDNAtools_overview.png
man/figures/logo.png
man/filter_mutations.Rd
man/get_background_rate.Rd
man/get_bam_SM.Rd
man/get_bam_chr.Rd
man/get_fragment_size.Rd
man/get_hist_bins.Rd
man/get_mutation_read_names.Rd
man/get_mutations_fragment_size.Rd
man/get_mutations_read_counts.Rd
man/get_mutations_read_names.Rd
man/get_read_counts.Rd
man/merge_mutations_in_phase.Rd
man/mutations.Rd
man/positivity_test.Rd
man/simulator.Rd
man/summarize_fragment_size.Rd
man/targets.Rd
man/test_ctDNA.Rd
man/vcf_to_mutations_df.Rd
man/verify_tag.Rd
tests/testthat.R
tests/testthat/test-ctDNAtest.R
tests/testthat/test-fragment_size.R
vignettes/.gitignore
vignettes/bibliography.bib
vignettes/ctDNAtools.Rmd
