aab54f7f7a435c7ebd65de75e352be50 *DESCRIPTION
396908995adc564db5b0bfa897c1fb0f *NAMESPACE
765b37da0bde11e61b504081c4faef4b *R/Cluster_selection.R
5dcd25b4e4c13e696195f14e8133a52d *R/EM.R
a73c8d97c465b67c01ece9ea134bea5d *R/FlashQC.R
107e2fd2424c53102cc804bb953e6350 *R/Phylogeny_tree.R
320c66f464961d3886c8f27f004c629a *R/QuantumCat.R
992aa390ec613b64dbae407eff57c604 *R/QuantumClone.R
d475e7ef40bcf3b88aba006166451a54 *R/Tree_generation.R
272187db30a1650bdc4ea76d372bbec0 *R/data.R
a9cc0b20f6ff17601a0e6f7b3ab5d885 *R/descent.R
0eff7a58bbeac310b52108108f9b5419 *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
02d2b767977d3082f8a84e39b36bddf7 *inst/doc/Release.Rmd
3f5889fbcc3aee4951d67b50c751a6e1 *inst/doc/Release.html
aaffd3f5b8bb350d52322d3d90c03b04 *inst/doc/Use_case.R
901a310beb779dc2650b8e05687ecade *inst/doc/Use_case.Rmd
31d511bb5e96a4c5af2a41f14fe88488 *inst/doc/Use_case.html
254f85f5f1e4bc42329dd3bba56b9e32 *man/BIC_criterion.Rd
05098f1a26f0883799619410243dac4c *man/BIC_criterion_FLASH.Rd
2c9e316002fef4a461c22df92f2d0c1c *man/Cellular_preclustering.Rd
9d358ae6700eda13954b58c179a8c028 *man/CellularitiesFromFreq.Rd
6966d9f4e93801d54e152d689efcc9ee *man/Cluster_plot_from_cell.Rd
675b9ecbfea914f9ac9ec738b3bff944 *man/Compute_NMI.Rd
a6a0d5a8bb51d027726cb7a977b453f7 *man/Compute_objective.Rd
d036acb30a6b9c3284a1ad66170b2f5b *man/Create_prior_cutTree.Rd
77d82078490eae3a9a0f8b413ef9a1cf *man/EM.algo.Rd
401e7734e42c91f753d68a74b200772d *man/EM_clustering.Rd
28e6c37d78156df0b99a0dc6c84c6a5f *man/FLASH_main.Rd
92e91ab59ae5370c365e1a0e98cfab0c *man/FlashQC.Rd
c0742f6ca4b7c8f98ffe8715ab17e63a *man/From_freq_to_cell.Rd
16255785a82b1039be1b3128884531ef *man/FullEM.Rd
1b46174983fb85e97745fcb586c75357 *man/Input_Example.Rd
bc03a2baa0d1ec7db80e9367fc2fe3c4 *man/MajorityVote.Rd
54ef074767af99d4ff6ae2ea238569b5 *man/NMI_cutree.Rd
8701ed4ea72c34c5d89ffe2ae987b47b *man/One_D_plot.Rd
eb4742c123c7f0bdb5efaddcab850f85 *man/One_step_clustering.Rd
d40fc0fe0412c114cfc83a4017e17709 *man/Patient_schrodinger_cellularities.Rd
9b9ce68faad41b807c8d39cc3ce30fb0 *man/Precision_Recall.Rd
2dd315945cd75ecd650b658f7ef4b959 *man/ProbDistMatrix.Rd
b8282e4c4c7a09ce305f3383fc7ac2f2 *man/Probability.to.belong.to.clone.Rd
5c0c71493aec82a03c3d53b2dc0d9ef4 *man/QC_output.Rd
90573b3ccbe2033fc4e4a337ccd2e240 *man/QuantumCat.Rd
c97f472c4044ace4793ecdcd56e3b08b *man/QuantumClone.Rd
f1e9896d6a6266ade8f2102732833937 *man/Tidy_output.Rd
35119cc9358b8d1af76f0f4820daefcd *man/Tree.Rd
07916bb19f2ca96aaaa7f7a46b028356 *man/Tree_generation.Rd
898260868776d42a6a9f460af84d32f2 *man/add_leaf_list.Rd
41d034bfc82c81308af8ff4c827779cf *man/check_leaf.Rd
f2a9fd97b3c27dc80c74dc5e39ba1a89 *man/check_split.Rd
d286014407a224b933a807c454ee5b73 *man/create_priors.Rd
3e127d2a5429b6765984b9c54a63bfc1 *man/e.step.Rd
8cbe82eb16a1fcfd9a47db906f148701 *man/eval.fik.m.Rd
fb27f3654ec4884ae336753f4e32ce10 *man/evolution_plot.Rd
8885344cb975546163bb3a5ad9749dd2 *man/filter_on_fik.Rd
f2507913dd25211cdda64560a75c0d7c *man/find_x_position.Rd
db067ed3503eece357834abc3addadd5 *man/grbase.Rd
0f3445beb0b89fb8c6596d8c38819631 *man/grzero.Rd
0093af173771d62f5fc09ddf93a28f09 *man/hard.clustering.Rd
798e30c20fd7792578105c29b0c0ff50 *man/is_included.Rd
d9e88a886452b51ca403c1c89b12448c *man/list_prod.Rd
76dd9f5cee10be1ec500454f47e93ba3 *man/longueur.Rd
c68c6da6b0c257193148ccfc6e4154c7 *man/m.step.Rd
21fb79251ae4c9d00be4321001dd2425 *man/manual_plot_trees.Rd
d1d69b771056a5004ed904fc448e4fab *man/multiplot_trees.Rd
d10bc2fecd8662bec46ff1b587bb1861 *man/parallelEM.Rd
d2a5dd7c13e8a5f77cfed079be0494c7 *man/phylo_tree_generation.Rd
bac0db5b54b5a20b599389c3c6261fd3 *man/plot_QC_out.Rd
da7db0597fa2448e93e15db7180af921 *man/plot_cell_from_Return_out.Rd
385888cfacd5cfced809ec1f8e75a5bc *man/plot_with_margins_densities.Rd
b92839b4ac79b2ef350e4a6ead2cfedc *man/strcount.Rd
7e516cad992e6d84136c988f52811232 *man/update_probs.Rd
bc21656c9b41a740f240b46cb3f5d625 *man/zscore.Rd
d9bb18a78b22842c8ee09eb5da092cf6 *tests/reproducible_testing/Comparison_other_methods/Pipeline_test.zip
9b30407c31631250436c5f8304bd2ca5 *tests/reproducible_testing/Comparison_other_methods/Plots.zip
1622f25d63bcdfbef95e8b81ac6f2013 *tests/reproducible_testing/Rscript/Figure3.pdf
47e03b62884c2bbaf417d92ecd1d2435 *tests/reproducible_testing/Rscript/data.df
49c17b9654ce16d63d72f7cc2d636ace *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
02d2b767977d3082f8a84e39b36bddf7 *vignettes/Release.Rmd
901a310beb779dc2650b8e05687ecade *vignettes/Use_case.Rmd
