7295f74d574e025bb1d4d08645d43ba2 *DESCRIPTION
1ebbd3e34237af26da5dc08a4e440464 *LICENSE
01dd10bb662f1173302726fa3bdbf615 *MesKit.docker.md
a1263724bfa9ba5812cab2fd10918d2c *NAMESPACE
32e8a7436b6fb9b3ef407a4345b04944 *R/Meskit.R
b192d668931f919f913e61d5b85dc365 *R/calFst.R
27e6e8f6645b0cbb7ec7489e48909706 *R/calJSI.R
7a38023e5a66fb3d7336a4f4bc7a2b5f *R/calNeiDist.R
5f90fb853140a83379eb00b75d05b03a *R/ccfAUC.R
2e5c7534ff50ebdba367941b32baf215 *R/classS4.R
912cf8d942548c3ebe2838082ee18d43 *R/classifyMut.R
109b41836d144f30658eca66da4bcafe *R/cna2gene.R
6e5ecc3b2b4f7c220f9c38307151ebb1 *R/compareCCF.R
48900744eae5080a12eb6780cc3b19b7 *R/compareTree.R
8bee5132ab07546be6e5b873691d0256 *R/copyNumberFilter.R
6f8bb8b48876b3adacb67705707afc00 *R/defineMutType.R
71eb8411044c1fa8c59befc990c38b9f *R/drawVafCluster.R
510d109a6a3e51379d0bf2e7a2aa879f *R/fitSignatures.R
418fef65b1297e860a5cab8373b189a3 *R/getMutMatrix.R
b5eb409152e4b40cb6b18dd835286305 *R/getPhyloTree.R
bede188424d9fa1b51d29224c18cfaf7 *R/mathScore.R
fd8678034b33c3ace5022ff13dfea968 *R/methods.R
55528c7766e51b4d35837cc4241aa3cf *R/mutCluster.R
47b376e2a9564723dd44ab45f3754685 *R/mutHeatmap.R
cfa7e731f6cdf93b3cd9ef276ea550ef *R/mutTrunkBranch.R
d190f40c0f601f07143eff095930bbe8 *R/phyloTreeAnno.R
67813af00ec48b6527f46bd01bcde41b *R/phyloTreeObject.R
ec8715eedd110dae0338253f28194c68 *R/plotCNA.R
24652999e1f082440c5a651436780159 *R/plotCorr.R
fa84893f24b9805a4d5f3cca89fa2fb2 *R/plotMutProfile.R
c673d3a1732686922225661ab0997e7a *R/plotMutSigProfile.R
31578740612662361962a575aaad63f7 *R/plotPhyloTree.R
ac11763ab9eb081ad8deee71cd64ad97 *R/plotPowerLaw.R
c49b8c948532ef37440966cb96f85a24 *R/readCCF.R
3eb4586bda8d583461b08f347b69f947 *R/readGistic.R
9cf5443eaec6ccb0dba368afb0db26d0 *R/readMaf.R
69367fb9b5699c52b3b97f49b4eb782a *R/readPhyloTree.R
07c368b9ec459e75fb908c4dc4bc733e *R/readSegment.R
974f2dce3587f94e3106a191dc80614a *R/subMaf.R
f4a0b761847dd26728780cd91024708f *R/subPhyloTree.R
cc9ad3465dc1eb60d6a33d1ef7b44ba1 *R/subTriMatrix.R
8aeb71d91c8e9739b556e3ff2017bf17 *R/testNeutral.R
0bf95d1e205ddf2cb45ea65d74f1b6de *R/triMatrix.R
500a70405dbdb20f5ac5e4f84a601af9 *R/validation.R
68f22f512edc7b2c2f9105c0ca0b8d07 *README.md
e6e193252a5d68f9c9eac35b027adefd *build/vignette.rds
bbb1add69784e37a665baf396e88b480 *inst/NEWS
1c9d14f9c5a3f921251734ada4edbc1a *inst/doc/MesKit.R
ee9fdade1f795d99d69ed58607c9a7d6 *inst/doc/MesKit.Rmd
94cb0690a6a047c10aa21d7ae2a187b7 *inst/doc/MesKit.html
73475c69d50a8abbc5003c6e3fbcc1de *inst/extdata/COREAD_all_lesions.conf_99.txt
bbf1e42df7b342e819b48232e9d0d68a *inst/extdata/COREAD_amp_genes.conf_99.txt
fd83f06be6020795a6b453796382036e *inst/extdata/COREAD_del_genes.conf_99.txt
5bdcaf3ff5882c3de7026f47dec38c25 *inst/extdata/CRC_HZ.ccf.tsv
eed935c4fda91359832edc4c4a1aef9d *inst/extdata/CRC_HZ.clin.txt
477c455f8ca51d6ac0e13456abbe4c1e *inst/extdata/CRC_HZ.maf
c1ec49b2e5288fb7e622e128ac250a30 *inst/extdata/CRC_HZ.seg.txt
1df1e2385c47c6ea75b63be0482d8bdd *inst/extdata/IntOGen-DriverGenes_COREAD.tsv
c8ca223fcfef444096ae3f527356be7f *inst/extdata/signatures.cosmic.rds
7207c9f423908046fc188f42e3454b4a *inst/extdata/signatures.etiology.rds
bc5935304abda95d788802f35e7c3fff *inst/extdata/signatures.exome.cosmic.v3.may2019.rds
fed50b039f3c4a1fb5fed7768ecdd2b2 *inst/extdata/signatures.nature2013.rds
5b67b29040734bd56ac967ab12be5266 *inst/script/DATASETS
e285402f3565aa9ce185b3e796eb7152 *inst/shiny/dom/ccf.CSV
d99fe9de18f20abd0107c959ae39766f *inst/shiny/dom/maf.csv
8c081cc279d772c5d36e10045543539c *inst/shiny/server.R
1e0bcf508d06aba61a9a4cd679ef462c *inst/shiny/ui.R
59e22dcf8d8365ab2b2f489af0d14edd *inst/shiny/www/css/main.css
61ecfad7b9fd8ef695ae64d2974a336c *inst/shiny/www/image/MesKit_workflow.png
77bd4e2ee47328a37c333c50b6221ef1 *inst/shiny/www/image/button.png
1036afa1e6045ab20e414d6555e6e613 *inst/shiny/www/image/logo.jpg
48fb7a78e9b55f128072deccadf4b5a6 *inst/shiny/www/main.css
5eb5bd6b29db8fac2e122ef17fd92455 *man/Maf-class.Rd
4d251e479076b203e487d1bafdc7e662 *man/MafList-class.Rd
5014e6f8b5e015e5c80c7a1daf9bdc4b *man/calFst.Rd
bf13c6cba29c499976ea1358d19b0126 *man/calJSI.Rd
82195cb545ef4fc2ea9f56da3ed36a4b *man/calNeiDist.Rd
d5d74b267c7e5c19ccdaad8a4413afa5 *man/ccfAUC.Rd
cc51aa702d52eb4861f1f455730715aa *man/classifyMut.Rd
e2114d0fe544d1d6f172c091639d55c7 *man/cna2gene.Rd
d4af8b2932765b8d632ed3436f5af5fa *man/compareCCF.Rd
4038fad3b711ef210bb46d8af9626eed *man/compareTree.Rd
0239fb477f54af0b2b486dbeb68843f3 *man/fitSignatures.Rd
72ac115e3fe27c9b7a55ac41fae854c9 *man/getBinaryMatrix.Rd
c5dad00b496e9a5ee6aa1051edfc05ff *man/getBootstrapValue.Rd
aad395c03b97c12ea2d18aa77eb2f66a *man/getBranchType.Rd
740cab9833cd083c1fe3b83c5311ac57 *man/getCCFMatrix.Rd
bbe5015945dc642eb89b2c747172ff8f *man/getMafData.Rd
71ceafccb9b77622461c37776a3fa2e6 *man/getMafPatient.Rd
1affc8bf9b1bbca5120c23ac4d5d393b *man/getMafRef.Rd
c3f8adddfc8d8596850e7c96e7cfdc43 *man/getMutBranches.Rd
68b86a4850271bfedac8cff3c487d9bd *man/getNonSyn_vc.Rd
08ec4ead32a1f7107bcb4e8ddcf6c51c *man/getPhyloTree.Rd
dff7cb23a950d0dc58daa8c6416c9dff *man/getPhyloTreePatient.Rd
15036b3e0eafee4c0578afed22ed10a9 *man/getPhyloTreeRef.Rd
4d3bfdf8dbf68bd51d8756582d9ec5ad *man/getPhyloTreeTsbLabel.Rd
9b5edd45d8b5993e5a902cd66f2c2625 *man/getSampleInfo.Rd
71c0a1a00a0fc45c058f2801786419fe *man/getTree.Rd
c9d621365fb2a37e3d77d35a6379482c *man/getTreeMethod.Rd
8f2e8a811d85974db4b00cd3f3c2287d *man/mathScore.Rd
ad63159fc4e84681798b589722a2ae0c *man/mutCluster.Rd
f1f60b0948f59896d247f0c28d466b5a *man/mutHeatmap.Rd
70176df6ad2123779e92d3b5f0155c58 *man/mutTrunkBranch.Rd
c5ee56d0e892ce12379544d3ee308b39 *man/phyloTree-class.Rd
be8639ed2b90a7dec7e7a74379dca8ab *man/phyloTreeList-class.Rd
571217595b515d37796e33ead3d7666c *man/plotCNA.Rd
e33456be1a71a0f7fdbf007a71f6e58b *man/plotMutProfile.Rd
ede3fdce12885b6396fb29174055660b *man/plotMutSigProfile.Rd
29dfe4e02efdf446054a8b83c6e23634 *man/plotPhyloTree.Rd
2b8fe4dad2c98c39d15d5597d4fa4525 *man/readMaf.Rd
9bcf3b53b28f4a5f6b061b976bd7cb24 *man/readSegment.Rd
b318648044f0cf20752857127110b078 *man/runMesKit.Rd
72c9f61bf81b5e73cda826b130cb078c *man/subMaf.Rd
65495b0f7d89c4b5aaa77c6626ca048a *man/testNeutral.Rd
8728c0361177a42d2659f50295afe458 *man/triMatrix.Rd
ee9fdade1f795d99d69ed58607c9a7d6 *vignettes/MesKit.Rmd
61ecfad7b9fd8ef695ae64d2974a336c *vignettes/MesKit_workflow.png
2844188baa397107c1251f35cea72eac *vignettes/logo.png
