Files in grailbio/conta
Detect cross-contamination
.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/RcppExports.R
R/conta_error_model.R
R/conta_ethnicity.R
R/conta_functions.R
R/conta_graphics.R
R/conta_likelihood.R
R/conta_loh.R
R/conta_main.R
R/conta_parsers.R
R/conta_source.R
R/conta_swap.R
R/conta_threshold.R
README.md
example/.gitignore
example/170501_cfDNABRH1308323_Conta_0_01.collapsed.nobaq.tsv
example/170501_cfDNABRH1308323_Conta_0_025.collapsed.nobaq.tsv
example/170501_cfDNABRH1308323_Conta_0_05.collapsed.nobaq.tsv
example/170501_cfDNABRH1308323_Conta_0_1.collapsed.nobaq.tsv
example/170501_cfDNABRH1308323_Conta_0_6.collapsed.nobaq.tsv
example/170501_cfDNABRH1308323_Conta_0_8.collapsed.nobaq.tsv
example/170501_cfDNABRH1308323_Conta_1.collapsed.nobaq.tsv
example/README.md
example/clean.sh
example/combine.sh
example/run.sh
example/run_small.sh
example/test.collapsed.nobaq.tsv
scripts/conta_ethnicity.R
scripts/conta_find_source.R
scripts/conta_graphics.R
scripts/conta_run.R
scripts/conta_swap.R
scripts/conta_threshold.R
scripts/generate_default_metrics.R
src/.gitignore
src/RcppExports.cpp
src/genome.cpp
src/genome.h
src/intersect.cpp
tests/testthat.R
tests/testthat/clean_up.sh
tests/testthat/helper-test_data.R
tests/testthat/test-conta.R
tests/testthat/test-edge-cases.R
tests/testthat/test-error_model.R
tests/testthat/test-ethnicity.R
tests/testthat/test-filters.R
tests/testthat/test-functions.R
tests/testthat/test-intersect.R
tests/testthat/test-likelihood.R
tests/testthat/test-loh.R
tests/testthat/test-parsers.R
tests/testthat/test-sex.R
tests/testthat/test-simulation.R
tests/testthat/test-source.R
tests/testthat/test-strand.R
tests/testthat/test-swap.R
tests/testthat/test-thresholds.R
tests/testthat/test_data/dbSNP_art_subset.vcf
tests/testthat/test_data/source_test/170410_cfdna_100T_34795B_1.subset.collapsed.nobaq.tsv
tests/testthat/test_data/source_test/170501_cfDNABRH1308323_Conta_0_01.subset.collapsed.nobaq.tsv
tests/testthat/test_data/source_test/170501_cfDNABRH1308323_Conta_0_025.subset.collapsed.nobaq.tsv
tests/testthat/test_data/source_test/170501_cfDNABRH1308323_Conta_0_05.subset.collapsed.nobaq.tsv
tests/testthat/test_data/source_test/170501_cfDNABRH1308323_Conta_0_1.subset.collapsed.nobaq.tsv
tests/testthat/test_data/source_test/170501_cfDNABRH1308323_Conta_1.subset.collapsed.nobaq.tsv
tests/testthat/test_data/source_test_double/170410_cfdna_100T_34795B_1.subset.collapsed.nobaq.tsv
tests/testthat/test_data/source_test_double/170501_cfDNABRH1308323_Conta_0_01.subset.collapsed.nobaq.tsv
tests/testthat/test_data/source_test_single/170501_cfDNABRH1308323_Conta_0_01.subset.collapsed.nobaq.tsv
tests/testthat/test_data/test.1000G.vcf
tests/testthat/test_data/test.baseline.tsv
tests/testthat/test_data/test.context.tsv
tests/testthat/test_data/test.dat.tsv
tests/testthat/test_data/test.dbsnp.vcf
tests/testthat/test_data/test.edge.3.tsv
tests/testthat/test_data/test.error.tsv
tests/testthat/test_data/test.female.bio-metrics.txt
tests/testthat/test_data/test.filtertm.gt.tsv
tests/testthat/test_data/test.filterwgbs.gt.tsv
tests/testthat/test_data/test.genome.fa
tests/testthat/test_data/test.gt.loh.tsv
tests/testthat/test_data/test.male.bio-metrics.txt
tests/testthat/test_data/test.pileup
tests/testthat/test_data/test.posterior.txt
tests/testthat/test_data/test.regular.maf.tsv
tests/testthat/test_data/test.sim1.gt.tsv
tests/testthat/test_data/test.sim2.gt.tsv
tests/testthat/test_data/test.sim3.gt.tsv
tests/testthat/test_data/test.supp.maf.tsv
tests/testthat/test_data/test.targeted.maf.tsv
tests/testthat/test_data/test.tsv
tests/testthat/test_data/test.vcf
tests/testthat/test_data/test.wgs.maf.tsv
tests/testthat/test_data/test_strand_dbsnp_neg.tm.vcf
tests/testthat/test_data/test_strand_dbsnp_pos.tm.vcf
tests/testthat/test_data/test_strand_for.tsv
tests/testthat/test_data/test_strand_rev.tsv
