Files in QuantumClone
Clustering Mutations using High Throughput Sequencing (HTS) Data
MD5
DESCRIPTION
NAMESPACE
inst/doc/Use_case.R
inst/doc/Release.html
inst/doc/Use_case.html
inst/doc/Use_case.Rmd
inst/doc/Release.Rmd
vignettes/Use_case.Rmd
vignettes/Release.Rmd
R/data.R
R/plots.R
R/FlashQC.R
R/validation_tools.R
R/Tree_generation.R
R/QuantumClone.R
R/EM.R
R/QuantumCat.R
R/Cluster_selection.R
R/descent.R
R/Phylogeny_tree.R
man/BIC_criterion_FLASH.Rd
man/Compute_objective.Rd
man/list_prod.Rd
man/One_step_clustering.Rd
man/grbase.Rd
man/Tree_generation.Rd
man/NMI_cutree.Rd
man/Create_prior_cutTree.Rd
man/parallelEM.Rd
man/From_freq_to_cell.Rd
man/Input_Example.Rd
man/BIC_criterion.Rd
man/update_probs.Rd
man/create_priors.Rd
man/FullEM.Rd
man/Precision_Recall.Rd
man/strcount.Rd
man/Compute_NMI.Rd
man/Tidy_output.Rd
man/manual_plot_trees.Rd
man/check_leaf.Rd
man/eval.fik.m.Rd
man/EM.algo.Rd
man/find_x_position.Rd
man/Cluster_plot_from_cell.Rd
man/Probability.to.belong.to.clone.Rd
man/plot_with_margins_densities.Rd
man/QuantumCat.Rd
man/phylo_tree_generation.Rd
man/multiplot_trees.Rd
man/zscore.Rd
man/ProbDistMatrix.Rd
man/plot_cell_from_Return_out.Rd
man/QC_output.Rd
man/MajorityVote.Rd
man/EM_clustering.Rd
man/check_split.Rd
man/plot_QC_out.Rd
man/Cellular_preclustering.Rd
man/hard.clustering.Rd
man/Patient_schrodinger_cellularities.Rd
man/FLASH_main.Rd
man/evolution_plot.Rd
man/Tree.Rd
man/CellularitiesFromFreq.Rd
man/e.step.Rd
man/grzero.Rd
man/One_D_plot.Rd
man/longueur.Rd
man/filter_on_fik.Rd
man/m.step.Rd
man/QuantumClone.Rd
man/add_leaf_list.Rd
man/FlashQC.Rd
man/is_included.Rd
build/vignette.rds
tests/testthat.R
tests/testthat/test-ProbBelClone.R
tests/testthat/test-FlashQC.R
tests/testthat/test-One_step_clustering.R
tests/testthat/test-gradienttools.R
tests/testthat/test-plots.R
tests/testthat/test-validations_tools.R
tests/testthat/test-QuantumCat.R
tests/reproducible_testing/Comparison_other_methods/Pipeline_test.zip
tests/reproducible_testing/Comparison_other_methods/Plots.zip
tests/reproducible_testing/Rscript/reproduce.R
tests/reproducible_testing/Rscript/figure3.Rmd
tests/reproducible_testing/Rscript/data.df
tests/reproducible_testing/Rscript/reproduce_2.R
tests/reproducible_testing/Rscript/html_outputs.zip
tests/reproducible_testing/Rscript/filtering_pipeline_PoC.Rmd
tests/reproducible_testing/Rscript/optim_vs_optimx.R
tests/reproducible_testing/Rscript/filtering_pipeline_PoC_2.Rmd
tests/reproducible_testing/Rscript/parallelization.Rmd
tests/reproducible_testing/Rscript/Figure3.pdf
tests/reproducible_testing/Rscript/filtering_pipeline_comp_time.Rmd
data/Input_Example.rda
data/Tree.rda
data/QC_out.rda
