a578db4659bf54c9577228031f089350 *DESCRIPTION
a7dddcdf71792745b82aee651e8f6e04 *NAMESPACE
dd152aed168e4062351ab484fc29ff4b *NEWS.md
74e3a8518b7b6d9542a38e25bf08efe2 *R/calculate_best_shifts_stretches.R
99ecada595f809de511ac6b0d9471189 *R/calculate_distance.R
fc6cdf1aa7a0530fdc4752d92fd51a34 *R/get_shifts_extreme.R
4db693b958e9ec7659f86bba99820160 *R/greatR-package.R
83d47ec6060ba3a6713bf332b1a35a19 *R/optimisation.R
a1d9bcf6985ca5bad973dc380750921f *R/prepare_data.R
c8fe4ba9e272e2be4563403a5fa4773d *R/process_data.R
c141e9b499df40617a41ec31c6ab5175 *R/shift_and_stretch.R
6ae9fce84885c31672369dc171a723fc *R/summarise_results.R
fa393844b5190d6464c70c3fcc1b8149 *R/utils-calcs.R
b8a7af1dd0c58a426a8cadd004a09237 *R/utils-data-table.R
65cef5e0674056f6fc07dd2b3ca85c13 *R/utils-pipe.R
354fd9624072db7f496d774170afc537 *R/utils.R
8c078ff7649294a25284f5d4d2f1fb3a *R/visualise_result.R
0896de3c49f7e8fd8e3354f932d8876f *README.md
00b562b1e48501b33cd934fc7650dbb6 *build/vignette.rds
7def38171d202d577a0d8ac206347983 *inst/doc/optimise-parameters.R
911a31522126e1b3f88b1807dcad9303 *inst/doc/optimise-parameters.Rmd
1faa681e47621b0316535869f3057362 *inst/doc/optimise-parameters.html
76491e08d205d36e9c480bc3b2bf0b82 *inst/doc/prepare-data.R
9870b2e411ab6c844f1174d8feb5f41c *inst/doc/prepare-data.Rmd
1c2c0b4aa3833ceec3efe6b24acdcaa4 *inst/doc/prepare-data.html
29c2f71f9024018c21fe3ca4e931a85d *inst/doc/register-data.R
48a2ff4b45ad6dde11a8851ed16746c5 *inst/doc/register-data.Rmd
f5f03adfbbff7603c8dd8bf94b78ae78 *inst/doc/register-data.html
bcf484e6a9fb8c8696dac4d38b9adc9f *inst/doc/visualise-results.R
c3ab5f1d24817840f967f1a7bf2ec0a4 *inst/doc/visualise-results.Rmd
99bf28201976ba75e1140020c2d8e6be *inst/doc/visualise-results.html
a99ef28f6e666f9282c59c20187dbfb0 *inst/extdata/brapa_arabidopsis_all_replicates.csv
fd0b7bc05f1b110c17909514bb17cbe9 *inst/extdata/brapa_arabidopsis_mean.csv
dfb2324dfa561fd1671f138f05d683a6 *inst/extdata/sample_data/arabidopsis_expression.rds
025aac55fc6afb73605b89ff39705264 *inst/extdata/sample_data/arabidopsis_expression_5genes.rds
a5bd04b77db0c00d93731a4d0a92c9dc *inst/extdata/sample_data/brassica_rapa_expression.rds
a834436f45fecc809121efa5e94c5d83 *inst/extdata/sample_data/brassica_rapa_expression_5genes.rds
b510e99e4e4362551fcd0a0deda08f42 *inst/extdata/sample_data/id_table.rds
a10aba62c9873a69ae48b0466a90bdc5 *inst/extdata/sample_data/id_table_5genes.rds
dc294e7c4bc67bbe1b483c3df5ed53ac *man/calculate_between_sample_distance.Rd
b390cf54b6b770694d3f6758774d8041 *man/figures/greatR_workflow.png
dc28c4e5541b71bd9652e8719b4d795e *man/figures/logo.png
ba2f84377a3f7e5132f9d09b8becd1af *man/get_approximate_stretch.Rd
e0d3fea15dd2a33f9c0eb9e06d787062 *man/get_expression_of_interest.Rd
f75fec3e15f30afafe11f28a0b7a0eb4 *man/get_mean_data.Rd
d2728575f266cf394fc321b40a315304 *man/optimise_registration_params.Rd
4894ca10756199e25f914bfd34f517b0 *man/pipe.Rd
b92873959d68d90e6ab45bbf184b0b4d *man/plot_heatmap.Rd
9002adf104bd0c42679c5fa0a1429e05 *man/plot_registration_results.Rd
0d05ae0e309ce7342b9f62fd01ec9157 *man/scale_and_register_data.Rd
77a1c775586076d17dd07baca9242856 *man/summary_model_comparison.Rd
d6025d03d394eab4b6753b4931b6a96c *tests/testthat.R
7dd8a28f186d8e1d8648e894bdbabc15 *tests/testthat/test-optimisation.R
25dde2b444ceb8994394b582b000df97 *tests/testthat/test-prepare-data.R
f901490bf9a9cb1142291637656be6d8 *tests/testthat/test-process-data.R
aecc2e2fdcfce2ccc6be80760bdc63b2 *tests/testthat/test-utils-calcs.R
0a402ce546cba5e6c0d720e8c25a33e0 *vignettes/figures/all_data_illustration.jpg
1398bd39cea37efd437d2e1f6e5aeb68 *vignettes/figures/mean_data_illustration.jpg
75843b9da7510438df1ed89c73fb3b25 *vignettes/figures/optimisation_workflow_with_initialisation.png
fd07e0cad43367f90bf6a95fcfacfedc *vignettes/figures/optimisation_workflow_without_initialisation.png
74525183b54aff5b6299f57bc0e809b3 *vignettes/figures/prepare_data.png
7f3f752623632c22b4d5f63b842dcf9a *vignettes/figures/reg_results_with_boundary_init.png
dedcdb5a9dd72633b9e4a26e83c47ebf *vignettes/figures/reg_results_without_boundary_init.png
177089938cd701fc90ad960688bb4ddb *vignettes/figures/registration_process.png
a350dc9bf1fc5e0840be20cdde224b64 *vignettes/figures/visualisation_process.png
911a31522126e1b3f88b1807dcad9303 *vignettes/optimise-parameters.Rmd
9870b2e411ab6c844f1174d8feb5f41c *vignettes/prepare-data.Rmd
48a2ff4b45ad6dde11a8851ed16746c5 *vignettes/register-data.Rmd
c3ab5f1d24817840f967f1a7bf2ec0a4 *vignettes/visualise-results.Rmd
