256b4cbe33a2778d62646334695e4e1d *DESCRIPTION
495b9c4aba3ffcd0dc68cb80e39d513e *NAMESPACE
765b37da0bde11e61b504081c4faef4b *R/Cluster_selection.R
5dcd25b4e4c13e696195f14e8133a52d *R/EM.R
a73c8d97c465b67c01ece9ea134bea5d *R/FlashQC.R
107e2fd2424c53102cc804bb953e6350 *R/Phylogeny_tree.R
ea2544d3ec88336bc07febbc766bd6be *R/QuantumCat.R
9acf862cc44f9b2fa3306fe586562863 *R/QuantumClone.R
d475e7ef40bcf3b88aba006166451a54 *R/Tree_generation.R
272187db30a1650bdc4ea76d372bbec0 *R/data.R
a9cc0b20f6ff17601a0e6f7b3ab5d885 *R/descent.R
2997c42ac7693688a44135bcb507a858 *R/plots.R
4167b01c75d2abe612e8402f26966330 *R/validation_tools.R
0811848fa5af1aecfb358a327b82f7d0 *build/vignette.rds
7134d836575307a8314a6c05a9914c23 *data/Input_Example.rda
7799d6f42e6db8d78ef29ba677c637f9 *data/QC_out.rda
059186d5bac4c8d0fb8ae917f42e2a02 *data/Tree.rda
3fadd0c63e2490b81b98ee3c591e27ca *inst/doc/Release.Rmd
cc89cfecb9051bb8af25f03e33d2183d *inst/doc/Release.html
f465d51ef702140a7235a4099d1c74ce *inst/doc/Use_case.R
25375d0bcaf27c89919dfed5079fd411 *inst/doc/Use_case.Rmd
0d837984b02862a3dd391607d735ba6c *inst/doc/Use_case.html
4426ddd4d47ba2aa2ca87e9754f4adcf *man/BIC_criterion.Rd
6260bf02c9cbdf942d8cc8334c84336c *man/BIC_criterion_FLASH.Rd
207a38c25bee129fea5f7b20ced969c0 *man/Cellular_preclustering.Rd
9f71252687cd4e85c6999ab629bd7e60 *man/CellularitiesFromFreq.Rd
eaf5be18be7e4289fe8d8a4b7bb51e6d *man/Cluster_plot_from_cell.Rd
35dfeb8042a612302824747da7263fe0 *man/Compute_NMI.Rd
5a9ecee3bc9ab97fb25c0e661e713915 *man/Compute_objective.Rd
c29e2d98c7f4ede0168e1b510dd6e57f *man/Create_prior_cutTree.Rd
4348f83adf4957af7bce19b4b781fe68 *man/EM.algo.Rd
d959d0aafec336579cdb0dc54b32750c *man/EM_clustering.Rd
d44b3ea6e083e90f7c41c571e2d6f589 *man/FLASH_main.Rd
bb126113cc8e33c7dd5363adbf29abb7 *man/FlashQC.Rd
9ab1eb5f093226ff012ef51010991734 *man/From_freq_to_cell.Rd
f5e1491c5984d4f2590531925c23d2f4 *man/FullEM.Rd
a521546ed47dde55c0169fe53e0fdbf0 *man/Input_Example.Rd
c8202b701e8bfad9cb129118aa3ff7d4 *man/MajorityVote.Rd
63ec760d6d9b232ae17c1238f27e6247 *man/NMI_cutree.Rd
c7ea446c7a113fb0355ead5886482d2b *man/One_D_plot.Rd
5f398f6bbb0a1db7dee6f10bad3a1fe2 *man/One_step_clustering.Rd
b3eeb541e465a8d717959bc0ca6c4e44 *man/Patient_schrodinger_cellularities.Rd
b1920f914dea4405fa8ed9b7cdebe6f3 *man/Precision_Recall.Rd
8ad3be841af82e93cae1acb81b6c93aa *man/ProbDistMatrix.Rd
2187b3d8f0b1d120e2d8dfa466b2caf9 *man/Probability.to.belong.to.clone.Rd
ef631da0664dc8daff35f7e33e52e854 *man/QC_output.Rd
9e562ddb8b5d27fddf0cd5ccadacb912 *man/QuantumCat.Rd
378458fd0500b1b81d14f1a24634fe06 *man/QuantumClone.Rd
e4dfdc98e55aae52499bdf6a5a7ce8a9 *man/Tidy_output.Rd
bd1afbbafa47567e183123066ab1f86f *man/Tree.Rd
fbaed9d181fd15e00e4c5b8219505b0a *man/Tree_generation.Rd
75210959b69ca027b5ccb6609df8f7a7 *man/add_leaf_list.Rd
cb865cfefc0ebed8609c6e947490800e *man/check_leaf.Rd
ea2f30c6c49919e5dcc871f7b352d20b *man/check_split.Rd
cea856574a0639ef54ced3cf59706695 *man/create_priors.Rd
7ddcf965d9af43ba76b146422c2fe707 *man/e.step.Rd
78b46cb8416d58d3fb230e6283091f30 *man/eval.fik.m.Rd
c587fff1382a72f3a1fdc8cf56d5caca *man/evolution_plot.Rd
5e038dff4ca2a38dcb8adb997cbab432 *man/filter_on_fik.Rd
2effd418036426eff877ded79e63df83 *man/find_x_position.Rd
ed05ac02d9a630394ee299dfd57b64ed *man/grbase.Rd
604d0a9abfc8bfbfe55bc94cae3f2c3e *man/grzero.Rd
50247741d2d14ebbda0276e872b3bd81 *man/hard.clustering.Rd
e21f7f027b2931c383874ef52291d07a *man/is_included.Rd
f7032877e0a5598631ec8d04b64c0983 *man/list_prod.Rd
3ac99cb13a302b8f4090a797c50af038 *man/longueur.Rd
6763259f6bfe97e864f87e3598d6e677 *man/m.step.Rd
b532d5444a922b664ade2ade7786fee6 *man/manual_plot_trees.Rd
778b41fe7f616ea4b2f6ae399e6d2bb5 *man/multiplot_trees.Rd
8a707cdb496ec16a7fb6387d64f3f184 *man/parallelEM.Rd
c77977c3207e702e6471ee11506ffedf *man/phylo_tree_generation.Rd
48bd3cb35b517f11dac9d85ff3459bf8 *man/plot_QC_out.Rd
03bef9547929ed0791421e0dfb4f2c2a *man/plot_cell_from_Return_out.Rd
1341b18340a432d53ac4f0c505c432c2 *man/plot_with_margins_densities.Rd
4edc3d3668780b1fbee31f0f8c61d936 *man/strcount.Rd
9f821d7e9d47cf23836def460c9c0ac5 *man/update_probs.Rd
8a9ef0957caafcbbdbc3acdd2fe2045f *man/zscore.Rd
d9bb18a78b22842c8ee09eb5da092cf6 *tests/reproducible_testing/Comparison_other_methods/Pipeline_test.zip
9b30407c31631250436c5f8304bd2ca5 *tests/reproducible_testing/Comparison_other_methods/Plots.zip
2c14433ea514d704394cacc2a9119f96 *tests/reproducible_testing/Rscript/figure3.Rmd
3306389f1e56d045992f5c850d0a25f3 *tests/reproducible_testing/Rscript/filtering_pipeline_PoC.Rmd
c576978e93f50566e65d09a124da6700 *tests/reproducible_testing/Rscript/filtering_pipeline_PoC_2.Rmd
c5d65acce07d38fb20025abc20fc1898 *tests/reproducible_testing/Rscript/filtering_pipeline_comp_time.Rmd
d59f0e81546211d7a72adde801bdeae8 *tests/reproducible_testing/Rscript/html_outputs.zip
08ea86b3f59d358efe8e04a09a4f126e *tests/reproducible_testing/Rscript/optim_vs_optimx.R
bbbdcee13cbf1a4660109a60f3c5654b *tests/reproducible_testing/Rscript/parallelization.Rmd
2d0422740de42b82d4e9920d2d2feeb0 *tests/reproducible_testing/Rscript/reproduce.R
08ef5e1e2170ea3c84e94159204a6be9 *tests/reproducible_testing/Rscript/reproduce_2.R
dc0577e7bbd55af64b601f6d1b691950 *tests/testthat.R
45c7c60db1a420f0892ec3b649327775 *tests/testthat/test-FlashQC.R
ea28cb508c9a8b191f4f5002d0992df2 *tests/testthat/test-One_step_clustering.R
6ebc0043f8b35a56ea9fdfc1e6aa9b5a *tests/testthat/test-ProbBelClone.R
9d44694fc769b945435c5f26fe1a37b5 *tests/testthat/test-QuantumCat.R
97512d8a3bffb112695117134c429a82 *tests/testthat/test-gradienttools.R
c5e50366cd77f86e2c6e299ee6a83ace *tests/testthat/test-plots.R
7562bd63f0e39e30714e851b6153839a *tests/testthat/test-validations_tools.R
3fadd0c63e2490b81b98ee3c591e27ca *vignettes/Release.Rmd
25375d0bcaf27c89919dfed5079fd411 *vignettes/Use_case.Rmd
