Files in redsnic/CIMICE
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
.Rbuildignore
.git.bfg-report/2022-03-12/14-49-22/cache-stats.txt
.git.bfg-report/2022-03-12/14-49-22/deleted-files.txt
.git.bfg-report/2022-03-12/14-49-22/object-id-map.old-new.txt
.git.bfg-report/2022-03-12/15-00-42/cache-stats.txt
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.git.bfg-report/2022-03-12/15-00-42/object-id-map.old-new.txt
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.git.bfg-report/2022-03-12/15-02-12/cache-stats.txt
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.git.bfg-report/2022-03-12/15-02-12/object-id-map.old-new.txt
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.git.bfg-report/2022-03-12/15-08-32/object-id-map.old-new.txt
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.git.bfg-report/2022-03-12/15-10-19/cache-stats.txt
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.git.bfg-report/2022-03-12/15-17-38/cache-stats.txt
.git.bfg-report/2022-03-12/15-17-38/deleted-files.txt
.git.bfg-report/2022-03-12/15-17-38/object-id-map.old-new.txt
.git.bfg-report/2022-03-12/15-17-38/protected-dirt/641ba0b7-HEAD.csv
.gitignore
DESCRIPTION
NAMESPACE
R/CIMICE-R.R
R/DatasetGenerator.R
R/analysis.R
R/input.R
R/inputVisualization.R
R/outputUtils.R
R/preprocessing.R
R/weights.R
README.md
inst/NEWS.Rd
inst/extdata/example.CAPRI
inst/extdata/example.CAPRIpop
inst/extdata/paac_jhu_2014_500.maf
inst/script/fileDescriptions.txt
man/CIMICE.Rd
man/annotate_mutational_matrix.Rd
man/binary_radix_sort.Rd
man/build_subset_graph.Rd
man/build_topology_subset.Rd
man/chunk_reader.Rd
man/compact_dataset.Rd
man/computeDWNW.Rd
man/computeDWNW_aux.Rd
man/computeUPW.Rd
man/computeUPW_aux.Rd
man/compute_weights_default.Rd
man/corrplot_from_mutational_matrix.Rd
man/corrplot_genes.Rd
man/corrplot_samples.Rd
man/dataset_preprocessing.Rd
man/dataset_preprocessing_population.Rd
man/draw_ggraph.Rd
man/draw_networkD3.Rd
man/draw_visNetwork.Rd
man/example_dataset.Rd
man/example_dataset_withFreqs.Rd
man/finalize_generator.Rd
man/fix_clonal_genotype.Rd
man/format_labels.Rd
man/gene_mutations_hist.Rd
man/get_no_of_children.Rd
man/graph_non_transitive_subset_topology.Rd
man/make_dataset.Rd
man/make_generator_stub.Rd
man/make_labels.Rd
man/normalizeDWNW.Rd
man/normalizeUPW.Rd
man/perturb_dataset.Rd
man/plot_generator.Rd
man/prepare_generator_edge_set_command.Rd
man/prepare_labels.Rd
man/quick_run.Rd
man/read.Rd
man/read_CAPRI.Rd
man/read_CAPRI_string.Rd
man/read_CAPRIpop.Rd
man/read_CAPRIpop_string.Rd
man/read_MAF.Rd
man/read_matrix.Rd
man/remove_transitive_edges.Rd
man/sample_mutations_hist.Rd
man/select_genes_on_mutations.Rd
man/select_samples_on_mutations.Rd
man/set_generator_edges.Rd
man/simulate_generator.Rd
man/to_dot.Rd
man/update_df.Rd
tests/testthat.R
tests/testthat/testPipeline.R
vignettes/.gitignore
vignettes/CIMICER.Rmd
vignettes/CIMICE_SHORT.Rmd
vignettes/networkD3.png
vignettes/visGraph.png
