c6a0bda6be4a1aee69caad83a30a9131 *DESCRIPTION
4d2fddc42231d0f6e96711227ec68b13 *NAMESPACE
073e41442110e6e61bd6fc97620b4fef *NEWS.md
fce9819703da6d401942c8d7fb19ebe2 *R/app.R
b0c8fcb88afd2f095ad2d7df5578373f *R/calculate_overdispersions.R
b184be5aa01004cda00c0c2e4f12cd05 *R/compute_p_values.R
b830ef9375f8f8c153906a4e6f406f57 *R/cpam-class.R
921e814b8f451744702eef5abaa943a6 *R/cpam-package.R
2c973fb858b5142c7a76f44c055323a3 *R/cpgam.R
25fe77f201c821f34352b73167d7b64f *R/estimateSizeFactorsForMatrix.R
312d70d0cefdfd7ce4910002e0b6f962 *R/estimate_changepoint.R
c647f9d2c5f4aa811bee5aafce832ee5 *R/fixed-effects.R
7365fde65c66e3655a9212e75f10401b *R/lancaster.R
11bb67d5fe4d43db58c579848bab6ea4 *R/plot-gene.R
64f8a06cc823585e3b32b10b9bb0d2f0 *R/predict_cpgam.R
e1a91064e13ffb03b88e70f741ded2fd *R/prepare_cpam.R
6db9f98aefd713cf2b721f516980ab0f *R/results.R
72cf1e9a7cfe013a270998333c322365 *R/select_shape.R
b56ff2b193ecba52f9ec7f3b10cca008 *R/utils-pipe.R
158a96ea79a502959406748b30d5ff71 *README.md
4454e632feb75ce4f508807d50b3b12f *build/partial.rdb
affa603f589837c1e39df9b6deb5eb39 *build/vignette.rds
9efb8c2d9988298b2b6c884d2a969e16 *inst/doc/cpam.R
22f4f60bae0532ff3450d2c1fa16a334 *inst/doc/cpam.Rmd
b3c37ee964f4248b9de6e0608dcc128c *inst/doc/cpam.html
202e964a1369651375ef8e0fac1fb042 *inst/extdata/count_matrix_example.rda
44e65141f091ae273c338da51676c2c2 *inst/extdata/cpo_example.rda
b2006b760ba6138fc3c549a8ebbc517a *inst/extdata/exp_design_example.rda
92742ffb42491a2ee6e5c5d07fffb7e0 *inst/extdata/exp_design_path.rda
1ba198f98597a620a4210565db16587c *inst/extdata/t2g_arabidopsis.rda
b7a35f97cd8ce385f4b14b613c68aa54 *man/compute_normalization_factors.Rd
f67552285f1531acf55c734ee60b1d90 *man/compute_p_values.Rd
69b103ae442256a85df36d8229ba9eea *man/convert_to_long_format.Rd
64ac1e64a50354c3978fe6fae6d1351a *man/cpam-class.Rd
d8bca7cd35abd7a082b4fd4996db3a92 *man/cpam-package.Rd
4a9e7c080bb028946b19806384307bb8 *man/estimate_changepoint.Rd
8879458723f3adb2a2b2153c4b2a0402 *man/estimate_dispersions_wrapper.Rd
f99eb4587beafb2d34a9df6421398859 *man/figures/example_gene_plot.png
e8f2bef5f9e1a014cb20033cc8d3d71a *man/figures/example_trends.png
35cf8d8b2bd48b6b42993451cbea7752 *man/figures/plant_success_logo_horizontal.jpg
d8e5ad30fa60ac56d28012f9fe852767 *man/handle_gene_aggregation.Rd
b672c85e8e236cf35fd026d574c3c3bb *man/import_count_data.Rd
b22aa1bcdc79cfdf490662a116b17a25 *man/ose_rule.Rd
8f4aad003a999fae004ba9361f9a99d6 *man/pipe.Rd
09e137f86b85dd750f37c2b27b9a57eb *man/plot_cluster.Rd
fc5f21e2ee5e0f10508c81a0aa650885 *man/plot_cpam.Rd
be69726b6c354bbb4e3e1e9d9c5335c5 *man/prepare_cpam.Rd
3d24f3543ddf1ef47e1f0c3c3255ba1d *man/process_bootstrap_data.Rd
2e599c01bfd9053b720b8807e4ddc2d4 *man/process_count_matrix.Rd
80f7718734b0c037c2d42bc891e8d707 *man/results.Rd
eb64d3267b69bae3607837d9872f7c30 *man/select_shape.Rd
2df2bac73a8f499af1689c30915c6330 *man/simulate_p_mvn.Rd
ef4440187319f59eca4dcda288612f48 *man/summarise_bootstraps.Rd
3cd9adae0c6b793a070df94a75a24347 *man/ts_filter.Rd
3e35d138e8eee43ae82e822c2ea71e33 *man/validate_cores.Rd
d1df1708edd76cdf5ac093ab7e02242b *man/validate_inputs.Rd
e46fbc82f0537d661e1a3f8742a7170d *man/visualise.Rd
1912a63155ac25a035e93ad867f3e304 *tests/testthat.R
94d5f0276ad3f3d899d1d4a38075f51a *tests/testthat/test-app.R
0c624486bf88ac5e5f899a7e23f4960f *tests/testthat/test-compute_p_values.R
321bc1fff0b026d5ba87565e14a407e8 *tests/testthat/test-cpgam.R
6ffb136ad0dcb21bed1492f7dd4e7322 *tests/testthat/test-estimate_changepoint.R
1834c34e44a10e73a81b39ab45266a4a *tests/testthat/test-fixed-effects.R
17f6e3ebac17e2ea9f09b894e6007c51 *tests/testthat/test-plot-gene.R
95149bbfe6cfe087e224cee6866e5335 *tests/testthat/test-prepare_cpam.R
d53e159e01cb534ab7a1d9aab7d09c24 *tests/testthat/test-results.R
22f4f60bae0532ff3450d2c1fa16a334 *vignettes/cpam.Rmd
ac5e963ed8de3f58f80caf83aaebf4b6 *vignettes/cpam_cache/html/__packages
8a6f9a63aa4b7ba9eda9f3482d7be82e *vignettes/cpam_cache/html/clusters-1_8883dd44465b101e6cd05ff73e9ec829.RData
6d23030633e241888117951ebba70520 *vignettes/cpam_cache/html/clusters-1_8883dd44465b101e6cd05ff73e9ec829.rdb
3d9273888309474e2d5739fededb7f6e *vignettes/cpam_cache/html/clusters-1_8883dd44465b101e6cd05ff73e9ec829.rdx
b7c07ae223cb4d30377c48c7b77d1d55 *vignettes/cpam_cache/html/clusters-2_7dd4df92554ca4b23d80d948cb33317b.RData
d41d8cd98f00b204e9800998ecf8427e *vignettes/cpam_cache/html/clusters-2_7dd4df92554ca4b23d80d948cb33317b.rdb
449753d2396ba21cc818b8c94d6e8806 *vignettes/cpam_cache/html/clusters-2_7dd4df92554ca4b23d80d948cb33317b.rdx
52512e4492d5d44a66873383272b4c82 *vignettes/references.bib
