aedd8f06e21f12fbc6dea719213225e6 *CODE_OF_CONDUCT.md
bbad12c5420ca3c7ae9f35c3fab4a118 *DESCRIPTION
1ebbd3e34237af26da5dc08a4e440464 *LICENSE
b57418694eb83c29a564aa558c32487c *NAMESPACE
60984455f184bf334e8e26b71795260b *NEWS.md
8081509f0b5b4ac39f8e5d731a486cbe *R/AllClasses.R
bb993e9527ab31773fb4f356c71241c5 *R/AllGenerics.R
b40d07548c04fdfed86597fe2a4241d4 *R/RcppExports.R
62e72432ffdc97e7e4cc1298dd4bb343 *R/TSENATAnalysis_methods.R
186936c383125c959fa0248766af26a8 *R/analysis.R
75f23a3aff662098d5ae7213404eda6f *R/assumptions.R
0de1e9a7e84f02a3ea5a14915322a20b *R/bootstrap.R
70953bb50b2e84b0ded69fcc67e6668e *R/bootstrap_ci.R
bca1822dc09148cbe70ce346787f1019 *R/bootstrap_diagnostics.R
0b530115dabef89bd91ebb157e4ba046 *R/bootstrap_divergence.R
d041d572c9ac52e09ea0aa08fc14d101 *R/bootstrap_divergence_helpers.R
e68f215e65ee37d88e443bdc3d246c5e *R/bootstrap_pipeline.R
33fff5b55f4123ff1d4a28ccd3df6a38 *R/divergence_core.R
6640c2aa1ba44d28d67e12d3d2aba57b *R/divergence_effect_sizes.R
3f7349232180a41d2203d857746c76a6 *R/divergence_helpers.R
69fd22f029d324c70b3bbf3c77fd867a *R/diversity_core.R
e406582484a021ece73466af55dc84e9 *R/diversity_helpers.R
417a161f96f9feb37e2b860007301346 *R/entropy_core.R
598ad1e2e03f925f750f933cedbb1237 *R/globals.R
0adfab70052d064e1513f322ef566ec2 *R/io_salmon.R
6c71668d7bc302f64f6cb4f17a26b4c5 *R/jackknife_diagnostics.R
6740aa09ea4f487b2c37f437805398ff *R/jackknife_isoform_switching.R
81b0ebc13885f787095551a9398f479c *R/jackknife_rcpp_wrapper.R
3e331e235e02860824cbddaae1874ab8 *R/lazy_load.R
0e53a4146dbbf57d52b7b413d5e1c7d4 *R/m_estimation.R
e28e5564900eac9055782c419f4a475a *R/orchestration.R
a76739d39531c73d101da0ad29f07524 *R/orchestration_results.R
c71038e60c42e6713e5bb5225a08e3bb *R/package.R
e270ecbf26a5f8977cab974559057d92 *R/parallelization.R
0135e6e2dbb8bae84171d6d42c43ea33 *R/plots_gam_helpers.R
7145d32cec472e81feebe30fe466fe1c *R/plots_heatmaps.R
828e5ff90d2918df8c5745327721db33 *R/plots_sait.R
b7f1cf5901011f11425e5fdd16a00045 *R/plots_spectrum.R
e9d48fdb5ffafccdbcea0a1f5717f31d *R/plots_stats.R
48fe9e4644deb3f21f5f46a89cfda3ac *R/plots_themes.R
810327098e1d9f460a92f659dccdf8d9 *R/plots_transcript.R
99942f1f286f78e51133b827d7579424 *R/plots_tsallis_q.R
2c47ca8aacd2de624d3e334658fee5da *R/plots_validation.R
a683593cd3f6a521b02e70aa68cbf7ef *R/plots_violin_density.R
44bf00e8464424165308e616b9be528d *R/rank_transform_core.R
7e294e4161046c3c504c359a37f8f247 *R/rank_transform_helpers.R
60b1b3b4c4153b2fda3337710871ffdf *R/readcounts.R
453ee90f66717f267d9d0c88ce462d33 *R/s4_class.R
18acdd7fc9495c8adab55de6150549df *R/s4_functions_assumptions.R
88c1fc9d7ef189e673f928f35b655956 *R/s4_functions_build.R
dd36e065b4eed6d9b253511a90cd0dd0 *R/s4_functions_concordance.R
f967b4a490247c4b18432174c75a0af0 *R/s4_functions_divergence.R
1adc9c5a18a9f44e4585211ae71a0817 *R/s4_functions_divergence_distribution.R
b04020c6d6f264645480933c4300772c *R/s4_functions_divergence_spectrum.R
f440cf995b37954c51cdb71ab6eaa2e5 *R/s4_functions_diversity.R
a510821f6329bd8464ab1481bd170894 *R/s4_functions_effect_size.R
5aa7c8a6b000ca7bc56c260edf4a7377 *R/s4_functions_expression.R
2a1aa3e9460ffb7672f5cb1700eda157 *R/s4_functions_filter.R
cfb241509e9cca0ece8f4c953718446a *R/s4_functions_jeo.R
b370388b3e4465763b7ee2d76141e1da *R/s4_functions_jis.R
48ea7f5049eec99e7a9f009c0e21850c *R/s4_functions_jis_delta.R
3fbb438d20ff6b0d2f78ce4b232021b4 *R/s4_functions_m_estimator.R
6cf4b8cf03e954cf61baf8864cedc451 *R/s4_functions_plot_concordance.R
a3e432535331e3f9ff810476d44900e8 *R/s4_functions_plot_sait.R
ed73ed090e854b79f9ac9ee727d32fef *R/s4_functions_rank_transform.R
300facdaab95ea6d9c22a601102e3f14 *R/s4_functions_sait.R
fde8853eca2c0b0d8a83835f90908237 *R/s4_functions_utils.R
297b8d91f31f08d0a98555065eff73cc *R/sait_core.R
dd824c60db9d6f908366b1ca5f3a4d9c *R/sait_fpca.R
82435ae1251fbc7a5f947f188d97b604 *R/sait_gam.R
84190da3a5270f8db0f85d5ef0eb39a8 *R/sait_gee.R
863841d44376a1c63a395ea55a31dd24 *R/sait_helpers.R
644f2095c80741717a1314dc68e36c41 *R/sait_helpers_fit.R
b3dfa2eb80c9708ec0f633e9baa3ade6 *R/sait_lmm.R
27a9113c4bdffb4f75e9fd808b3783a7 *R/se_manipulation_build.R
1165165c67a2462926abf32bd0b32c3f *R/se_manipulation_filter.R
132bdae7c9a14c7bc71fe005fdf814e1 *R/se_manipulation_map.R
290b1cc86251d14d469e43085952cc98 *R/validate_data_compatibility.R
f79b0531c3e49b29e4bdcd9eb10a9b6c *R/westfall_young_permutation.R
2fa2f713bd056b4a32596dc1ca66150a *R/zzz.R
f23cd8bfeee6299577895cd7cf4b9bb0 *README.md
9cb8b728f22ebcff9611085e747d4cb9 *build/vignette.rds
cab4ebd72fd1acb4a6e66776a3be8820 *data-raw/README.md
5ba1e50c39202466eba8b3f90d9af919 *data-raw/scripts/preprocess.R
6425ae50d4bf7b37fb152f401a0dbb72 *data-raw/scripts/salmon_pipeline.sh
23f98c034c7cea3a9e61e4094e1e054b *data/readcounts.RData
79658cbcb2a1e6689cb9567b5373075d *inst/doc/TSENAT.R
b64831a3711b3b6f0a5d49a387670c03 *inst/doc/TSENAT.Rmd
7e33f1ffbda87059cf4903ead93bae47 *inst/doc/TSENAT.html
0a3709f0ea76fe24a76bf015cf0390c6 *inst/doc/TSENAT_appendix_A.R
3f7266a2b0b672e5715bc028506d0037 *inst/doc/TSENAT_appendix_A.Rmd
5eae0b993b45c8ea7226ceba52de4e8b *inst/doc/TSENAT_appendix_A.html
b48e0baacc8ffb8e61dfb4946a266175 *inst/doc/TSENAT_appendix_B.R
4a5c0ff0447820f3d3d8022a20918071 *inst/doc/TSENAT_appendix_B.Rmd
f25515c67c6c0a1fd333f1f813e104e3 *inst/doc/TSENAT_appendix_B.html
dcdd30f24a628315b0ad483b61479c12 *inst/extdata/analysis_sait.rds
f736fc13f974f84f79218949c1f2710d *inst/extdata/annotation.gff3.gz
299fba79178c85d5b2b170e9d35b01cc *inst/extdata/gencode_subset_test.gff3.gz
18425fc6ea6c26c6b9db4b8d0909b07a *inst/extdata/gene_ids.tsv
f3988a6f95397ea4f88d2309516732e9 *inst/extdata/metadata.tsv
3d50d2affb9252d7f3e339795ab3fcae *inst/extdata/tx2gene.tsv
7bdf9a9de0dab40ccb9d30ff8972b617 *inst/scripts/README.md
055842f1b02becc999a80f7716b009fe *man/AllGenerics.Rd
fc5087f5010e836343f2cf93ae96f36b *man/TSENAT-package.Rd
1c0c92d226f872d5001b9bba5830e405 *man/TSENAT.Rd
99ed6b88043026bbe0be4ddb126cf092 *man/TSENATAnalysis-class.Rd
ee86e84bfe5c775db6eac342e08ba09b *man/TSENATAnalysis-metadata.Rd
e762cc403cf0802d953051afe652a865 *man/TSENATAnalysis-se.Rd
5aac0688fff7d0aa18ceb9f520b4c530 *man/TSENATAnalysis.Rd
acef14d2bf1f5447b47466d580ead5af *man/TSENAT_config.Rd
a5eb426164b1a2128c357608dfe880e8 *man/build_analysis.Rd
a22dd1c5c24aafa88036f51e23fa9a3c *man/calculate_assumptions.Rd
fbd0ef91ce4e5417f2c424d6c5dbd873 *man/calculate_concordance.Rd
b921296f3c22ca0fa695cda6d76a4ac6 *man/calculate_divergence.Rd
147d84d1e493ffcafb69a72d478667db *man/calculate_diversity.Rd
73fc2e008d3657dde987f251aca34f5a *man/calculate_effect_sizes.Rd
fbf52effe335409dc70e571be1aff384 *man/calculate_jeo.Rd
ce7ad43fb1c6cd17b227b86f8960fcba *man/calculate_jis.Rd
da1ac242a45ec08165b5e98f1cb45386 *man/calculate_m_estimator.Rd
71274c657c6475bc1cd1d4ca178f2857 *man/calculate_rank_transform.Rd
8d5644f8b3c35ea70144541fdbd2dbd3 *man/calculate_sait.Rd
27f7f33ba544ef542ea9dd3f9ebb4369 *man/filter_analysis.Rd
dd5b766b428312b866f7d2655c2a0a16 *man/plot_concordance.Rd
a1222774fce72e1443cfd91e21fb309c *man/plot_divergence_distribution.Rd
f4e9b343a85aaa2e7f7da7d0a4d3dae7 *man/plot_divergence_spectrum.Rd
60a89b8bda27238040fec03a2225b5ad *man/plot_diversity_spectrum.Rd
f569ed08c42f21ad638a40c08fc7220e *man/plot_diversity_violin_density.Rd
a4da0702e70997ecb115fe5b49df0165 *man/plot_expression.Rd
5316adb8965b81c9789f67534d2a7e96 *man/plot_jis_delta.Rd
89d9610294247a2a0c7dd0774062cbe2 *man/plot_sait.Rd
377f54170e8a6144f7f21cc24b8542e3 *man/readcounts.Rd
b6e9957e73a953cd5a7a60269245fbc3 *man/results.Rd
bfb9dbb4104e3c2097f3c3b3a3a3c23a *src/Makevars
5db53a0c0272184b2bec8c7b4267d994 *src/Makevars.win
3a7f2e30511d8f70dae6c3c437f60541 *src/RcppExports.cpp
94ce1f5e4c398eda68106f29dda08a1f *src/resampling_rcpp.cpp
ee94d8610f03a987dff16cfe7994ffdc *tests/testthat.R
45ea5c356bdf1bb3149d16e0720b3be0 *tests/testthat/setup.R
53f6cbe6a19311acfc0f5d83dce1eab8 *tests/testthat/test-assumptions.R
ca7e3983d693d08d7653300932529b3f *tests/testthat/test-bootstrap-core-helpers.R
7a1497efedf72ce5ca60ffbfec8e7ebd *tests/testthat/test-bootstrap-edge-cases.R
2fab7608b318b1b7951745e3b0a549ce *tests/testthat/test-bootstrap-entropy-ci.R
c1a202d109240ff43285cd15f828ae68 *tests/testthat/test-bootstrap-filtering.R
5562cce3200d316d3ad594b9614955ae *tests/testthat/test-bootstrap-multiq.R
6fc62cf54c13fd1cfcf13f65fad1cd34 *tests/testthat/test-bootstrap-quantile-fix.R
09d70f8e191b741aeb42b93033bd33f4 *tests/testthat/test-bootstrap_divergence.R
305fde967e186f4fd84193562b9405c0 *tests/testthat/test-code-quality-utilities.R
a1d34bf2462bc2a67bc1e6977ec9eb18 *tests/testthat/test-core-functions-divergence.R
83528cda062bdaa158113dad97e68cf9 *tests/testthat/test-core-functions-divergence_effect_sizes.R
59e492069e4a9f46efd9255ad7ce8f61 *tests/testthat/test-core-functions-divergence_helpers.R
21dca56ab167425091ee0854546392e0 *tests/testthat/test-core-functions-diversity.R
0a97e4e596d26cc55f0dbfe9e8f9fff4 *tests/testthat/test-core-functions-diversity_helpers.R
cffe3ad1dbf369f4fe4c35a4430cfd0c *tests/testthat/test-core-functions-entropy.R
50b5124628ba61af65a7589b60b072a6 *tests/testthat/test-core-functions-filter.R
0360939dba787dd2738d520c12a616bd *tests/testthat/test-core-functions-jis.R
88e51cdc46e6c2177cd21201a6dbb748 *tests/testthat/test-core-functions-map.R
b37fcb0ceac1f657431bde6655d0d3da *tests/testthat/test-core-functions-rank_tests.R
0f44f1716578f218bcbe03b753e3cbca *tests/testthat/test-core-functions-s4-divergence.R
a9ba584a9766fc1b58912fa4bacd936e *tests/testthat/test-core-functions-s4-diversity.R
7a454d069f94789d9434aeade8fc3674 *tests/testthat/test-core-functions-s4-jis.R
2bdbc84ecf8752345f6740986d70bf64 *tests/testthat/test-core-functions-s4-rank_test.R
fed856a2758039bbef641a8bfedd76e1 *tests/testthat/test-core-functions-s4-sait.R
355a7d4353a635dddf4402d4ec3c4040 *tests/testthat/test-core-functions-s4.R
8abac2caf643c4ce48fe594435300739 *tests/testthat/test-core-functions-s4_build.R
4037ae0b2b73b3b70ab2e2b120e53648 *tests/testthat/test-core-functions-s4_filter.R
9e19bc25ac22285ec2380bc7755591bd *tests/testthat/test-core-functions-sait.R
16b07400113784d06af70d028a7a7554 *tests/testthat/test-core-functions-salmon_io.R
90de8e9cf055af29beab62c60063ae6f *tests/testthat/test-golden-statistical-outputs.R
605a9ff9c0c438fae47f7fb9d9a0c4d6 *tests/testthat/test-infrastructure-performance.R
e30686b618148edfa2dc1a8f42173472 *tests/testthat/test-infrastructure-tsenat_config.R
a2a872b409d772863a3a890be46dc2ca *tests/testthat/test-infrastructure-validate_data_compatibility.R
90139d6bede5063f58319e53bb3e5a50 *tests/testthat/test-infrastucture-accessors.R
73b00532e41237096e9f3747cfda70da *tests/testthat/test-integration-orchestration_config.R
25a9b558e7a9edad07b5ab9734a944a6 *tests/testthat/test-integration-orchestration_results.R
1a8713ed3c5f63f4554d0a9a09a1661b *tests/testthat/test-integration-workflow.R
62ae78403a3c314fee289036330bb5ad *tests/testthat/test-lazy-loading.R
bcd7377b4e3a2d03414def805b530cc7 *tests/testthat/test-package-initialization.R
b5bf75c8ada0baaf6688ff095f6ca8a8 *tests/testthat/test-parallelization.R
66ef7790eb42d4b436e62cf9385c6077 *tests/testthat/test-print-s3-methods.R
76d6bb4d9d3eafe78ae10782939b2cc1 *tests/testthat/test-rcpp-bootstrap.R
f65e0a14c7d717505f6257be0c0dd801 *tests/testthat/test-rcpp-jackknife.R
d9c4aa88244af7db42db95a540d0bc96 *tests/testthat/test-s4-allclasses.R
4b2489a78810cba2aae94f7c81f43b0f *tests/testthat/test-s4-validation.R
ee457d8b5fd46acbe6fa12d391ddc550 *tests/testthat/test-statistical-methods-assumptions.R
238301bc271fdeeecf567ab0eb8c59a7 *tests/testthat/test-statistical-methods-concordance.R
aa40155d10d2bf05781de4254b22be88 *tests/testthat/test-statistical-methods-jackknife.R
bd93e69999466ac9a7589366d5b5fc91 *tests/testthat/test-statistical-methods-jeo.R
05339004ed931512440c7940fd7f1804 *tests/testthat/test-statistical-methods-jis.R
ba5458097798984b75531eff1830b534 *tests/testthat/test-statistical-methods-m_estimation.R
4f7398731abc5f234082ee654a54f0cd *tests/testthat/test-statistical-methods-rank.R
02878da061b00d14c23e3b3321c1883b *tests/testthat/test-statistical-methods-rank_art.R
838cfc7e5148aa45113dfb20d37654b3 *tests/testthat/test-statistical-methods-rank_kendall.R
1c633c64bee0efecb8c9fb449f8e292c *tests/testthat/test-statistical-methods-rank_multicorr.R
c1f12fb9727fde7db017781076aacc94 *tests/testthat/test-statistical-methods-sait.R
5fe60c12ad6fa7db05e3e07c346df6f0 *tests/testthat/test-statistical-methods-sait_fpca.R
778d85ffe2c8a72c9fd94102957ab0fd *tests/testthat/test-statistical-methods-sait_gam.R
39f5cf1d963d08a136685096d7b0703a *tests/testthat/test-statistical-methods-sait_gam_gamma.R
dcdaa254596288fe71f6581e6046d48a *tests/testthat/test-statistical-methods-sait_gee.R
9563d614f3d58f36675dcb7af1eda180 *tests/testthat/test-statistical-methods-sait_helpers.R
cd5ce317d3c0c2e4d644f07a2e978113 *tests/testthat/test-statistical-methods-sait_helpers_fit.R
7df46dd7d39d8cd171c3e94829611097 *tests/testthat/test-statistical-methods-sait_lmm.R
23ab70830666fb5a226501828e45c818 *tests/testthat/test-statistical-methods-shrinkage_estimation.R
6a91fd067911827209f173919c23e0d3 *tests/testthat/test-statistical-methods-westfall_young_validation.R
f08ab13401fc696cf14e327109fa4e9f *tests/testthat/test-text-formatting-utilities.R
c2f5ef3ba9fd0dbe385a820e7b0ad7e7 *tests/testthat/test-visualization-compute_stats.R
44c62f6da1ae1ea79e5c1187f6726e4a *tests/testthat/test-visualization-expression.R
18b395087cee3ccab9ea298a56a1ece9 *tests/testthat/test-visualization-gam.R
3dbf128e84f0bc88963148083790964f *tests/testthat/test-visualization-heatmaps.R
0024b19b68087fcebfeabe31fc480dea *tests/testthat/test-visualization-helpers.R
1bb536ec3a06a4712809bde9ec5e34b8 *tests/testthat/test-visualization-sait.R
23b818a9805c709d3a022ddab45abafb *tests/testthat/test-visualization-spectrum.R
14341f865718d86380e4acfcdf875b72 *tests/testthat/test-visualization-tsallis_q.R
ab0ca1bcc0c7a924abf0b5dcae26a180 *tests/testthat/test-visualization-violin_density.R
15d6935ce00061d99382e0236c797276 *tests/testthat/test-visualization-volcano.R
b14cf9bced471189bf1a71084e8c4348 *tests/testthat/test-visualization.R
0dfdaf37086422f6483d9837f6dccfee *tests/testthat/tests-factory.R
b64831a3711b3b6f0a5d49a387670c03 *vignettes/TSENAT.Rmd
79de78c1af2efceb8e2bd118c9ce0295 *vignettes/TSENAT.bib
3f7266a2b0b672e5715bc028506d0037 *vignettes/TSENAT_appendix_A.Rmd
4a5c0ff0447820f3d3d8022a20918071 *vignettes/TSENAT_appendix_B.Rmd
