Files in DeveauP/QuantumClone
Clustering Mutations using High Throughput Sequencing (HTS) Data
.Rbuildignore
.gitattributes
.gitignore
.travis.yml
DESCRIPTION
GUI_windows.R
Images/Cellularity1_1.png
Images/Cellularity_clustered1_1_1_2.png
NAMESPACE
R/Cluster_selection.R
R/EM.R
R/FlashQC.R
R/Phylogeny_tree.R
R/QuantumCat.R
R/QuantumClone.R
R/Tree_generation.R
R/data.R
R/descent.R
R/plots.R
R/validation_tools.R
README.md
appveyor.yml
codecov.yml
data/Input_Example.rda
data/QC_out.rda
data/Tree.rda
man/Cellular_preclustering.Rd
man/Compute_NMI.Rd
man/Create_prior_cutTree.Rd
man/FlashQC.Rd
man/Input_Example.Rd
man/NMI_cutree.Rd
man/One_step_clustering.Rd
man/Precision_Recall.Rd
man/ProbDistMatrix.Rd
man/Probability.to.belong.to.clone.Rd
man/QC_output.Rd
man/QuantumCat.Rd
man/QuantumClone.Rd
man/Tree.Rd
man/Tree_generation.Rd
man/evolution_plot.Rd
man/manual_plot_trees.Rd
man/multiplot_trees.Rd
man/plot_QC_out.Rd
man/plot_with_margins_densities.Rd
man/zscore.Rd
tests/reproducible_testing/Comparison_other_methods/Pipeline_test.zip
tests/reproducible_testing/Comparison_other_methods/Plots.zip
tests/reproducible_testing/Comparison_other_methods/README.md
tests/reproducible_testing/README.md
tests/reproducible_testing/Rscript/README.md
tests/reproducible_testing/Rscript/figure3.Rmd
tests/reproducible_testing/Rscript/filtering_pipeline_PoC.Rmd
tests/reproducible_testing/Rscript/filtering_pipeline_PoC_2.Rmd
tests/reproducible_testing/Rscript/filtering_pipeline_comp_time.Rmd
tests/reproducible_testing/Rscript/html_outputs.zip
tests/reproducible_testing/Rscript/optim_vs_optimx.R
tests/reproducible_testing/Rscript/parallelization.Rmd
tests/reproducible_testing/Rscript/reproduce.R
tests/reproducible_testing/Rscript/reproduce_2.R
tests/testthat.R
tests/testthat/test-FlashQC.R
tests/testthat/test-One_step_clustering.R
tests/testthat/test-ProbBelClone.R
tests/testthat/test-QuantumCat.R
tests/testthat/test-gradienttools.R
tests/testthat/test-plots.R
tests/testthat/test-validations_tools.R
vignettes/Release.Rmd
vignettes/Use_case.Rmd
