Files in yannchristinat/oncoscanR
Secondary analyses of CNV data (HRD and more)
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/data.R
R/input.R
R/oncoscanR-package.R
R/scores.R
R/sysdata.rda
R/utils.R
R/workflow_oncoscan.R
README.md
data/oncoscan_na33.cov.rda
data/segs.chas_example.rda
inst/extdata/LST_gene_list_full_location.txt
inst/extdata/Oncoscan.na33.r2.cov.processed.bed
inst/extdata/README.md
inst/extdata/TDplus_gene_list_full_location.txt
inst/extdata/ascat_example.txt
inst/extdata/chas_example.txt
inst/extdata/triploide_gene_list_full_location.txt
inst/scripts/run_oncoscan_workflow.R
man/adjust_loh.Rd
man/armlevel_alt.Rd
man/get_amp_segments.Rd
man/get_gain_segments.Rd
man/get_hetloss_segments.Rd
man/get_homloss_segments.Rd
man/get_loh_segments.Rd
man/get_loss_segments.Rd
man/get_oncoscan_coverage_from_bed.Rd
man/load_ascat.Rd
man/load_chas.Rd
man/merge_segments.Rd
man/oncoscanR-package.Rd
man/oncoscan_na33.cov.Rd
man/prune_by_size.Rd
man/score_avgcn.Rd
man/score_estwgd.Rd
man/score_gloh.Rd
man/score_loh.Rd
man/score_lst.Rd
man/score_mbalt.Rd
man/score_nlst.Rd
man/score_td.Rd
man/segs.chas_example.Rd
man/trim_to_coverage.Rd
man/workflow_oncoscan.ascat.Rd
man/workflow_oncoscan.chas.Rd
tests/testdata/LST_gene_list_full_location.armlevel_scna.csv
tests/testdata/TDplus_gene_list_full_location.armlevel_scna.csv
tests/testdata/ascat_example-empty.txt
tests/testdata/ascat_example.armlevel_scna.csv
tests/testdata/chas_example-empty.armlevel_scna.csv
tests/testdata/chas_example-empty.txt
tests/testdata/chas_example-noFullLocation.txt
tests/testdata/chas_example-withChr.txt
tests/testdata/chas_example-withDuplicates.txt
tests/testdata/chas_example-withSeparators.txt
tests/testdata/triploide_gene_list_full_location.armlevel_scna.csv
tests/testthat.R
tests/testthat/helper.R
tests/testthat/test-armlevel.R
tests/testthat/test-clean.R
tests/testthat/test-compare.R
tests/testthat/test-input.R
tests/testthat/test-loh.R
tests/testthat/test-lst.R
tests/testthat/test-mbalt.R
tests/testthat/test-nlst.R
tests/testthat/test-td.R
tests/testthat/test-workflow.R
vignettes/oncoscanR.Rmd
