39690a216588673518b0abe3e05339c9 *DESCRIPTION
04a5b3b99dfab4be8f1b2f85baea5ae9 *NAMESPACE
798d40957caace4b049e4f4acd0f10aa *R/CIMICE-R.R
d1ad466a5d8a0d9224aae87c92c3e6e2 *R/DatasetGenerator.R
63f7cf40996e8eaabc86db5cc2194546 *R/analysis.R
1158600c415926a6825183ae75ab35c9 *R/input.R
3dbc0936cd9b19c7d2c01492bd02bd05 *R/inputVisualization.R
7fa6acd67f5f230619b3a3f5ca1498b3 *R/outputUtils.R
f7fcd4e809985b130bbc0982eec758c0 *R/preprocessing.R
aa3cb4233713e19188e8fe297d2c96bf *R/weights.R
cfa1010252ef834ff092827498201880 *README.md
0fefa7b539597341a5fe48f022f70b8c *build/vignette.rds
9c529366dfa86068e3ab4e6413d2e828 *inst/NEWS.Rd
62e2d9ee6d65c4050c4b5b1f49390bec *inst/doc/CIMICER.R
f06445b7a15dc37508399ee4c483fd84 *inst/doc/CIMICER.Rmd
8229c6a6e6bfee759dae143b6f79cfec *inst/doc/CIMICER.html
0e7532c595c53bfead58dc360a511762 *inst/doc/CIMICE_SHORT.R
1857c7e2f8a256e4ddb6a0d59c2bff5f *inst/doc/CIMICE_SHORT.Rmd
56e415238df9ecb915af83ebe9a8b03d *inst/doc/CIMICE_SHORT.html
d47ec2f30dcd255d105eb4a21a6c87ed *inst/extdata/example.CAPRI
37a3d2293a202aaeafd7cf394c4a1299 *inst/extdata/example.CAPRIpop
121201334a1c518a8b072199335f7d3e *inst/extdata/paac_jhu_2014_500.maf
e7e30f942dc35d006670e988b23fd426 *inst/script/fileDescriptions.txt
3ddacc681180608dbb40e46e8e29e4f7 *man/CIMICE.Rd
025725489a04991ae2c582d48dcdc37c *man/annotate_mutational_matrix.Rd
d32edb58177b5dd593a511711bdad887 *man/binary_radix_sort.Rd
4702e49aae8ee4ab872476a73044a237 *man/build_subset_graph.Rd
c8f2d1f3e791020dce825b7547d294c9 *man/build_topology_subset.Rd
58b063217a8de480d001702303e77476 *man/chunk_reader.Rd
fd499995451e64e895820b56baac5498 *man/compact_dataset.Rd
776f8c4191c2894cfbc7ac981d59d15a *man/computeDWNW.Rd
7ec413f56113e61df7aad0389c52aa0d *man/computeDWNW_aux.Rd
8accf2bf9dcf36e289a03375d99d3056 *man/computeUPW.Rd
a647a5835753e93d2f026467d1c7740b *man/computeUPW_aux.Rd
0a67c595b7be375bc7d097e2175fc2ab *man/compute_weights_default.Rd
94937f1751f510c4801f42459160be17 *man/corrplot_from_mutational_matrix.Rd
8f49233c876aa5601a5a96886be6fd7f *man/corrplot_genes.Rd
0230c6e8cbeaa0c0b6758e169d5471bf *man/corrplot_samples.Rd
4787fe46c9e2581193b77b841a7580a7 *man/dataset_preprocessing.Rd
9002f3505c10f4ee17297eb517d1b71c *man/dataset_preprocessing_population.Rd
908f52a3f7ac4ed2d90662deb527a8d1 *man/draw_ggraph.Rd
b6d94d1aeb029bf91085ce6cc17c4bf4 *man/draw_networkD3.Rd
a2072da1b62242999bff5db5156fea97 *man/draw_visNetwork.Rd
4d37909a8f07622cc3932852cdcb905f *man/example_dataset.Rd
9abe073497861206648f3bce59e4ecb8 *man/example_dataset_withFreqs.Rd
ca0527be10d533317ea7c2003a4c5701 *man/finalize_generator.Rd
54943645241006e4fcd5df001afe593b *man/fix_clonal_genotype.Rd
46818a4aa09e1b5a11d27bf459f5ad08 *man/format_labels.Rd
c9fbaff1881e94d25c69bd4abbc02573 *man/gene_mutations_hist.Rd
6a64b2b42cab595701f13369b1cf9735 *man/get_no_of_children.Rd
126914c7915e1e726e5444194f7faceb *man/graph_non_transitive_subset_topology.Rd
a179a63900f225ddb2bcd9a9e7259acb *man/make_dataset.Rd
d32257f5ad3df80b7ff9b26701216129 *man/make_generator_stub.Rd
121c2c64f3686c69d3872a21972ff347 *man/make_labels.Rd
16646f2fdbec0e19591a399037b6d5c8 *man/normalizeDWNW.Rd
bf9f79a03057ac4f3fcf97e36d0db615 *man/normalizeUPW.Rd
14df2a2ea65271e1cb5d5e81a6512599 *man/perturb_dataset.Rd
3d073116f3dc8787d046c6e6f6483ff1 *man/plot_generator.Rd
33c8c34a8fcee2b561e9a83c691f58cd *man/prepare_generator_edge_set_command.Rd
286fbb7980a2621c9a8a9381e6b16576 *man/prepare_labels.Rd
cd71300bbbb9e1d23188b4fcaaea7f28 *man/quick_run.Rd
edf3ecd55aeba165d8fab119aca1fa43 *man/read.Rd
b179bd52c6fc390f4d69e3a806592224 *man/read_CAPRI.Rd
f0eaf85e9a86f30d8ee231b1decbad64 *man/read_CAPRI_string.Rd
6c0a074b1ea34369145bb59412779ef4 *man/read_CAPRIpop.Rd
ffcc97c5d77e9765aa13bb31483392d6 *man/read_CAPRIpop_string.Rd
af134319010bf75d16443dbb73c4dd8a *man/read_MAF.Rd
7b6ddce1838a3083dc679928cf1fafa1 *man/read_matrix.Rd
7d2b6b9ce39ef1d9e737c6c4eda1b327 *man/remove_transitive_edges.Rd
69bb5901652015a219a34839317c56c7 *man/sample_mutations_hist.Rd
c70f1755c66aa5c0e848258cd768718e *man/select_genes_on_mutations.Rd
d9d96ea228c30cdf705d9f40f7dd819c *man/select_samples_on_mutations.Rd
16009f5e2b8b578412a970def0ceb38b *man/set_generator_edges.Rd
4fbfb800a98d0194a9e0c33d2c978c82 *man/simulate_generator.Rd
ff9973a69f535ec300d853342e43cd2a *man/to_dot.Rd
a621a434b5d4d8c0121542e7b9c23a15 *man/update_df.Rd
a96bd01bc274e8fdbdcb2a13bb836f09 *tests/testthat.R
a077883c5b6dfe0fc2ed85a521fe41d1 *tests/testthat/testPipeline.R
f06445b7a15dc37508399ee4c483fd84 *vignettes/CIMICER.Rmd
1857c7e2f8a256e4ddb6a0d59c2bff5f *vignettes/CIMICE_SHORT.Rmd
cf3bda0f1731d7a2ea02f141014ac4dc *vignettes/networkD3.png
30cac6f09d3e5ce990d2c508c4d43565 *vignettes/visGraph.png
