4b83b6faeb53b4e3a7fd5a289e5b263c *DESCRIPTION
c49814d7007ef77152c49e5790cd73a8 *LICENSE
613db2f9ccb545df6a5ecb94f2151bff *NAMESPACE
527e6c1c24da987d7eef22ae5ab8ebb0 *NEWS.md
ed8fb60a21e6febccee25ccb1ef3de3d *R/accessors.R
fcd70e0b4e30e8b0334b272287e27ff3 *R/analysis_registry.R
1410f95277742bfa39bc95cb9e7d9244 *R/analysis_spec.R
fd95d8e8654025fa251a0ca9fbad9837 *R/biocohort-package.R
0dfef1790098aa22902b7acd31f81cc6 *R/bridges.R
c1baaa0c768132c38a4b69359c1904ab *R/check_paths.R
0a8bcacd6c19bde6daff04f236420bdb *R/classes.R
0f797b9141105b06519377d40231d2d4 *R/cohort-internal.R
48acdab6a3ee82098a182d1498559a5f *R/constructors.R
88d005c9b1374781b1dbeeb16dfe408b *R/corrections.R
8ae50911a4038a53035954319f61bf54 *R/data.R
1c90047b6187a0a06fcff9bf92710382 *R/derive.R
dd6eab19dc4f06fab960d756ab53ff60 *R/filter.R
9ab270fbb8673cbfdc238dd977208048 *R/groups.R
bfc5168c20fa2650a4c0e5fd28b64680 *R/io.R
e6957223456dbc30b8df9b802374e009 *R/liftover.R
437ca7a8829ed49f359040e262970e7e *R/load.R
6611f2835d95f87dc5721e8dbe27a405 *R/orthologize-cohort.R
77a0953e15103e304c94b2bf79b1c350 *R/orthologize.R
5cabdbf6f48358138da09babd809fa3f *R/orthologs.R
f8226554270f51b27eae6cf2ed6bae86 *R/pairs.R
f99b773bb4488e48de1ec3647d686c10 *R/paths.R
78ea761740bd488e32b765f735fb20ad *R/print.R
0a831485f9b69f42a279e4088ac1fe23 *R/qc.R
143d548a5a05d2dd8586816c1968c0a6 *R/sample_sheet.R
49e60e685659b79ba8fd4fe09a4363cd *R/study_yaml.R
ee0df8ceab629c6556825b56e3fcda4b *R/translation-result.R
509f53ff920f9162c3aa54029d0da44d *R/validate.R
6d74f06a69b8a1303b578cfc8f9f42aa *R/validate_manifest.R
a35fdaeba48224511500861b57743c3f *R/zzz.R
e27ddbb96b56acc8fc0f1da69c756a9e *README.md
971f413d9bc1139c7a3643cf42d565a0 *build/vignette.rds
cef8c7b905c4bb97950ca77b20458f38 *data/example_cohort.rda
b0db9b4bc3e919363691b842e7ff76f0 *inst/CITATION
89456309fb0300e02eae77450d57b0ab *inst/doc/biocohort.R
f9116b551b6f87e810d1753342590591 *inst/doc/biocohort.Rmd
0cba431b373b10dd7d6363dfc164e13c *inst/doc/biocohort.html
4f8bd692bd5c348aa2512639e959b362 *inst/doc/glossary.R
32f854cd766306b4859a967553e56e57 *inst/doc/glossary.Rmd
2c3ec0f81ae9b8fc9b8726021bc92047 *inst/doc/glossary.html
4f8bd692bd5c348aa2512639e959b362 *inst/doc/naming-conventions.R
7888466058993598cf2499c1349adc26 *inst/doc/naming-conventions.Rmd
ea3b8c619a6566038cc185d4057cfdb7 *inst/doc/naming-conventions.html
0b1e5358d54fc0fb1f2264f172e70999 *man/AnalysisSpec.Rd
bde9bf0247d125d87012194aae373bb9 *man/Cohort.Rd
9ad6ec094c9557ade07936fce4978a9d *man/Study.Rd
3af63d9f23a203361830fbd33a6a8a71 *man/Subject.Rd
5cf4c6fb2c6eb20f9fffa387acacde22 *man/TranslationResult.Rd
19eb79b5f8966da194274b103c88ca59 *man/analysis_files.Rd
25d59bb10b5d507f7f60c05049c59d7c *man/analysis_list.Rd
3e85ff543b505d9852bbd72700cfa7cb *man/analysis_register.Rd
53860245154c4917294982d334cbe832 *man/analysis_spec.Rd
edc9c6339529bb156e16151676087c9e *man/analysis_spec_new.Rd
41c187b313c40d4d7c9b43b6de7fa7fc *man/apply_corrections.Rd
52d970dbae96febf98fc6ee1c560df3d *man/as_coldata.Rd
084efc2a66bf35d13091502b085991e0 *man/biocohort-package.Rd
f25fa77f7559b2f1a3752da2a26dd7c6 *man/check_paths.Rd
fffb5fe074cbb4b7b2d872f120fc7aeb *man/cohort-subject.Rd
ea0919372c4032971dfa3b00ceec343f *man/cohort_contrasts.Rd
bea1bb4860676cd41939c32843df4ee7 *man/cohort_derive.Rd
b51b7bf3042435e8d0f339486e36ad83 *man/cohort_filter.Rd
36ef2dd23051f71073c1bad3678b1397 *man/cohort_groups.Rd
69e990aad538114143350f2dab3e4eaf *man/cohort_new.Rd
4dfcc67d7321fe21ca9fc251703f4ff2 *man/cohort_qc.Rd
a3b97c443b9acee1d7c0a3422fabfa1e *man/cohort_read.Rd
2b14f166db87ed47aa9aa9297ffd0456 *man/cohort_save.Rd
4fcd9847f97c32a449b3a878d787e0d1 *man/completeness.Rd
24c9108bd9c699bc10d478a5ffd044c6 *man/corrections_log.Rd
c9e4a34699f12dc8ecff3eb00220004e *man/derive_log.Rd
8dd792e0889a98e036e07cca04de908f *man/ensure_dir.Rd
90ed51c139b38baf127fdbfaa8201356 *man/example_cohort.Rd
1a25a1ff724798b3a42cf086e800ffd9 *man/figures/logo.png
0d461b13dded445b1e39de971f69d24e *man/figures/logo.svg
d684d4462484a8a9c8b4539b8b5929d8 *man/join_metadata.Rd
37e4e4737ce5bb5830e649ba3d8a8c68 *man/liftover_backends.Rd
73ba943631e1b2b2cf3cc4e8309c396c *man/liftover_crossmap.Rd
c3b2dcdae7c69115f8f448544ba9ee25 *man/liftover_intervals.Rd
b4154bac7bb92b1fd716440881c0f3bf *man/liftover_rtracklayer.Rd
0146c714a60a18cb8d265fd1cca5de90 *man/liftover_vcf.Rd
e053993c3cf2258ba2f53cee34e9d88d *man/load_analyses.Rd
9ff9a106b5b0b66b1fb7a33ac7f16e0f *man/load_analysis.Rd
b73a8d3fbae4206ba377bb8fb1ffa533 *man/manifest_from_wide.Rd
4d268318b9f179d51bda6c2dbb4b90fb *man/ortholog_babelgene.Rd
9f0ccb375c7abcf9e8e8f61e3d9ee0b9 *man/ortholog_backends.Rd
84e0adc75fa6c1c8b5b4b8729e98c14c *man/ortholog_genes.Rd
2f4e27e6fc01fafca35f6e8e2d49cf43 *man/orthologize.Rd
84c1938523b8097b9dd4ae8b487a6336 *man/project_path.Rd
adfb5d4587864c294ac95ef28c777140 *man/project_root.Rd
fbd5dc6556d56d36f37283b05c91e565 *man/qc_log.Rd
6a5e624d7e39ca0baa06a17aa2a9faf8 *man/read_corrections.Rd
fd54a221b0d275e5d5e4fe18b7033657 *man/read_dotenv.Rd
016f46e8af2920c2f8a2eb7e4a962f4d *man/read_manifest.Rd
69b15d3046f7d3ca143b51826a6adda2 *man/read_manifest_csv.Rd
d88561f86512d09f195e5353f89621bb *man/read_study_yaml.Rd
b879f75aa77b96e03765952654983be4 *man/register_liftover_backend.Rd
10c60d95e198bdfda097ba16166b70cf *man/register_ortholog_backend.Rd
b31e470be0e7ea43f304c19f1d57ff15 *man/sample_pairs.Rd
14fae671437828be4c2456c7c45e78b4 *man/sample_sheet.Rd
b8121e971f894c39313f6899750997d1 *man/sample_sheet_templates.Rd
145aca0b6daddcf915779364c8d4b09d *man/samples.Rd
8d16d341c7a94b1a43f370448f962ccc *man/study_new.Rd
97bde18092d6a934c30b5db5c7cbf536 *man/subject_new.Rd
2c75d52e68e0b1369b9cf81f18cc80e6 *man/subjects.Rd
eeef7730cc4586732ad5646653920482 *man/translate.Rd
573d08bc6ca467704f4802b80302fc97 *man/translation_report.Rd
be60f2302f415a369aad94664b4a08e3 *man/translation_stats.Rd
966cb43e7206fdc2ee5a488225df4366 *man/validate_cohort.Rd
3de14830ef96ad02477cfb9aa8a0f959 *man/validate_manifest.Rd
382ba674870588e405723149bcb76bc8 *man/write_manifest.Rd
9e94626a0cb71acf2cacef6a70bc7c2e *man/write_study_yaml.Rd
9906dbb674ee884f735aec1cc31d077f *tests/testthat.R
a9858e30c319b658bc4d44b522265e94 *tests/testthat/helper-cohort.R
3e0f9f608cfe6c1704c5550147da7640 *tests/testthat/test-accessors.R
d60d767711076073ae3a6a3f31a06503 *tests/testthat/test-analysis-registry.R
6743ca9a1ad45ce439469cfa8cda5a28 *tests/testthat/test-analysis-spec.R
c12acf33cca516cb6615bc3fce333d06 *tests/testthat/test-bridges.R
1a9b8dac1ec78c06712bd97e3807af3a *tests/testthat/test-check-paths.R
feccacfe8378ed3b957ff013b4949676 *tests/testthat/test-classes.R
7026726fef28827a4ceae8231a866c51 *tests/testthat/test-constructors.R
2fbb7bb5b1414c65c82b82dc22131801 *tests/testthat/test-corrections.R
8003657b7e215e295c72fccb2cc3faef *tests/testthat/test-derive.R
1f95edcc60176e9cdf8daf1e0b2bf944 *tests/testthat/test-filter.R
4fc8002d715a9d1c7e3cebcaba2ca23e *tests/testthat/test-groups.R
5add018980541bec4583bd70fcad6d4d *tests/testthat/test-io.R
e218c585f765249eb336499cb5b995c4 *tests/testthat/test-liftover.R
c8c6f5d69decb2d18cc2f8ff8ece9470 *tests/testthat/test-load.R
7d971bb7d49af7d59072fce3561f50b2 *tests/testthat/test-orthologize-cohort.R
7cd39b5be240a57faf65f24927bb13de *tests/testthat/test-orthologize.R
d252281c7697dd6b2d303f74566e224a *tests/testthat/test-orthologs.R
2173ddd0197f136ce14eb803f96bfde3 *tests/testthat/test-package.R
74db435faedb8b529c31d3ba180b8715 *tests/testthat/test-pairs.R
8743c3d0b61412ed6bddc17cadad5c01 *tests/testthat/test-paths.R
a634bc3e52c8abeda92919a730f34c25 *tests/testthat/test-print.R
3bfb34cf9f726debab1750268aae3056 *tests/testthat/test-qc.R
4b8b4d91caf407a76aa128d809956b85 *tests/testthat/test-sample-sheet.R
f3bf1142b47dc5d6457672a6cf0ed711 *tests/testthat/test-study-yaml.R
2bc38c8eb4ffa9d0fedd34506b9b66bb *tests/testthat/test-validate-cohort.R
4e9cc5a8a44b05ec5047d6e59a6adc04 *tests/testthat/test-validate-manifest.R
f9116b551b6f87e810d1753342590591 *vignettes/biocohort.Rmd
32f854cd766306b4859a967553e56e57 *vignettes/glossary.Rmd
7888466058993598cf2499c1349adc26 *vignettes/naming-conventions.Rmd
