3abaffc28aed219e2df969a79061c505 *DESCRIPTION
82576951c0abf97e3c1f7d6e0f59c725 *LICENSE
a7d9ecebbbd49458c4d864b0ad069587 *NAMESPACE
791903c6f1ce5b4786197b41ca9ba839 *NEWS.md
0b84f2e4358abb3ba0709a7fc2b05c04 *R/data.R
ed9faf40543f783ab2a8473c2935cac7 *R/input.R
365f301a91c175b72f8ed8b59a0b4c2c *R/oncoscanR-package.R
3619e6ead41588b74a09a734f243479d *R/scores.R
383c0ebc6d5ba9f4831539489de65300 *R/sysdata.rda
efe1195d735bb9813863c319655fd2c2 *R/utils.R
5d5ed738a6dd8a494d49318a4e3abb87 *R/workflow_oncoscan.R
1421ae7cb7e025016e89d21ee2c9b698 *README.md
bfc53208cd7bf707c8ef4dd99604fff9 *build/vignette.rds
844b89a402d8726e1063c003bcea3fe7 *data/cntypes.rda
e29573c0f2685eb661d8fcef149ae864 *data/oncoscan_na33.cov.rda
c7c01582d165724b4112b3d24d019ff8 *data/segs.chas_example.rda
6eb9ab639d26af5fe0e24d1b00419802 *inst/doc/oncoscanR.R
c32eb2dc8b6e3efb998b5582ac645f21 *inst/doc/oncoscanR.Rmd
eedbe12f92dd236bd7c824979b22f987 *inst/doc/oncoscanR.html
e8557a48b3d8da697a0364cd578aa43f *inst/extdata/LST_gene_list_full_location.txt
647b68fb291676c6db0ea0ad2bf41605 *inst/extdata/Oncoscan.na33.r2.cov.processed.bed
e319df9a1cfa99e6827d4b5b900b268a *inst/extdata/README.md
a5fc1daced25fbadbd4ca9f487875eed *inst/extdata/TDplus_gene_list_full_location.txt
f966ca4bab76b3880d6075c294383f57 *inst/extdata/ascat_example.txt
dd4aca8b29709496bbeb721e7d482416 *inst/extdata/chas_example.txt
67f727aa7f50b9de096dc1989108bd36 *inst/extdata/triploide_gene_list_full_location.txt
04ef50d1c493d1f22ff05ba029c77d73 *inst/scripts/run_oncoscan_workflow.R
26569af5bbbf2e21129bdecc0dbad898 *man/adjust_loh.Rd
5f6e39e2cbadaf6f591c0441d160aa66 *man/armlevel_alt.Rd
3655c8e58bcb0aeac7acaa7e7acf7361 *man/cntypes.Rd
c7798723f92bf34bd03f386023ecc92a *man/get_amp_segments.Rd
a69694a5666ab79e6706a7a8c46e435d *man/get_gain_segments.Rd
b3eaa89535857adde8b78a2c8b686587 *man/get_hetloss_segments.Rd
4083a21d6d7ad439a4a3162fbc33a6b8 *man/get_homloss_segments.Rd
0c378dbc560e8d07bda2d1959ff5685a *man/get_loh_segments.Rd
be3cb472fb9932618859a8326a2d239f *man/get_loss_segments.Rd
270d8c29577ffc210b619eb1721ec820 *man/get_oncoscan_coverage_from_bed.Rd
544af2e0620a17cca2ae1d11cfd15f0c *man/load_ascat.Rd
9725ee6041fb90fa844c0db78327a5d6 *man/load_chas.Rd
8d02076fea0f4f8e9f0b434cd41b7fc1 *man/merge_segments.Rd
829b2c1c48a99b49ff2716829a0711d2 *man/oncoscanR-package.Rd
8936c8735e6fb0a7e15ef3dbda039321 *man/oncoscan_na33.cov.Rd
0f5687285abc52a4b22b324f41cf31d5 *man/prune_by_size.Rd
ff18f1fb3eb7888198d76f0de674065f *man/score_avgcn.Rd
9544e4be5943067a49076a6a1696108a *man/score_estwgd.Rd
e04923c8a131d302176c50d8f28fabb0 *man/score_gloh.Rd
647bd1513f04a23ace652a38298971dd *man/score_loh.Rd
f41ef0706c44ecdcb3807486e46acc88 *man/score_lst.Rd
3d2815cb4f05705a8e27e17c9581140a *man/score_mbalt.Rd
7f12036692a172701e151d105fa1a989 *man/score_nlst.Rd
64754f973066b6ce53261c447ec9a255 *man/score_td.Rd
6a35913350b26d618338c887629a8dc6 *man/segs.chas_example.Rd
432fbf460d2bb9de25bf98f2353ed366 *man/trim_to_coverage.Rd
04a2f666269939fe0b6928120d04ceb8 *man/workflow_oncoscan.ascat.Rd
3b37698c338fc8c7484f5898aa31a4ee *man/workflow_oncoscan.chas.Rd
049cca16ffcd295590823420ed606728 *tests/testdata/LST_gene_list_full_location.armlevel_scna.csv
b957eccddf5d072534a444c3f9a40ce8 *tests/testdata/TDplus_gene_list_full_location.armlevel_scna.csv
f6c9982b7b1303c04e3e67ab8ffa5838 *tests/testdata/ascat_example-empty.txt
1af19186a1df7d26e34f470d4f3bfc0f *tests/testdata/ascat_example.armlevel_scna.csv
e17c305382f6bc2a56de5f2bbc5230e5 *tests/testdata/chas_example-empty.armlevel_scna.csv
b929402ecaa5a79db53ad569fff70ce3 *tests/testdata/chas_example-empty.txt
3f7ccf9efa729c46f8d27ecdf3666cbb *tests/testdata/chas_example-noFullLocation.txt
c158a64e194f21878b2964051e3ad3c5 *tests/testdata/chas_example-withChr.txt
a3a66fa2cb9bbd7ac68fdfb66c3b9a16 *tests/testdata/chas_example-withDuplicates.txt
585a91f8880191080e90405d6ba8fce2 *tests/testdata/chas_example-withSeparators.txt
015e23c5ca6ba930095bfaa8ad49133a *tests/testdata/triploide_gene_list_full_location.armlevel_scna.csv
77f608451e65b135a30fa460aa0c4c64 *tests/testthat.R
026c574da550edbff320b54ec0c0ba81 *tests/testthat/helper.R
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8f615345827dcdcc966f768ac8f5e6d8 *tests/testthat/test-loh.R
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01e575fdb95445b5fe93d14082045ccc *tests/testthat/test-mbalt.R
a509fc9f59a04198a05f662247b19067 *tests/testthat/test-nlst.R
d6584f4ecbe13633a2ad69d5a6d7b4a7 *tests/testthat/test-td.R
ce9f2c7eb84f696d4572e1b5d98406e4 *tests/testthat/test-workflow.R
c32eb2dc8b6e3efb998b5582ac645f21 *vignettes/oncoscanR.Rmd
