f6529db0e70015af5419314b2e26d352 *CITATION.cff
858c01a03282d6464787e3eb89d16ac3 *DESCRIPTION
d709ccc4b35cfb0b0ba637d1f7be201f *INSTALL
3c490296a7a7af0368d6d2e4d592aacc *LICENSE
a261d76628ba581296a639ab2a4c2af1 *NAMESPACE
8233e604edc8f0a9c6581993891d9412 *R/CBN2Path-package.R
ed978dd85aad4aa242e943c2d6da96e0 *R/CBN2Path.R
f443979f73f1dfae0e20f4b3afce9453 *R/PathwayAnalysis.R
f73877d292f84ffd15bc6074232ecf59 *R/Spock.R
3564e9a909fc29a96faad9ceb740b074 *R/bcbn.R
ee9f6edacd510d399ea305197dd1746a *R/ctcbn.R
6682acc065a047e36315d06cc923444d *R/hcbn.R
ddfe534e8c5dad0ebcafe96045f11302 *R/tcga.R
e725833d9897948f276189eacb2a973e *R/utils.R
321f75f5556438e3228282b32b095739 *R/visualize.R
9bde39913917f8a2ebc99c34c417a5bb *README.md
a6de8cce7193b4376ddf4ef365e5f515 *build/vignette.rds
8cdf4486bcfedc4dd9a99f91911d61f8 *cleanup
b470011a65ba98c3efd1defff752386b *configure
4a2d02aecb2d9519de7c46773be92cdc *configure.ac
641d03cd80cc5859597d9d0b64bdb4f1 *inst/doc/CBN2Path.R
1fb560e0c0b193598c07e1e0fd33a2f2 *inst/doc/CBN2Path.Rmd
228c7d241762bb7738e87a0c14e6f511 *inst/doc/CBN2Path.html
1c7fce9499b878fe8a15bb97cff7d77a *inst/extdata/BC.label
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dfb19c41808770231379deaf86d02193 *inst/extdata/BC.pat
181fec753faa4abfffa182da108d4f23 *inst/extdata/BC.poset
5027f89adc814c2d655d031e1a845533 *inst/extdata/BC.sim.pat
533e2fc99fb6282bc6f9c80b7bc23d56 *inst/extdata/BC.sim.time
8fcd5b598b09f29b723fd51b9e051fa3 *inst/extdata/CRC.label
1a7cff913f9e332554e799bb8b53c68e *inst/extdata/CRC.pat
7aee2b5a1a3798cf19b431e0d7009a77 *inst/extdata/CRC.poset
ed1b4da41427414cdd838a4a91f665f4 *inst/extdata/HIV.gps
dfb19c41808770231379deaf86d02193 *inst/extdata/HSD.pat
181fec753faa4abfffa182da108d4f23 *inst/extdata/HSD.poset
a015a6aa016cb84155cb07b274e1c1dc *inst/extdata/Posets.rds
dd38ac4074e31c6906aeecde3618b89e *inst/extdata/RCC.label
f0e5ef51e0d537602433ce0e7c1ff9cf *inst/extdata/RCC.pat
561ff895d18801000b322feff4b85f9d *inst/extdata/RCC.poset
515631ad63ed0bb5775a1332db77d3be *inst/extdata/hiv.pat
dff9c73fc65b44ff5953b6dd82d8f83d *inst/extdata/hiv.poset
c4be4bed62b5d1169f706dab7620824e *inst/extdata/hiv.prf
164409a59dcef79a67e5688da9a03465 *inst/extdata/prostate.pat
cc50d73593a6422a57752132d1fd07f5 *inst/extdata/prostate.poset
ae246e0d629cc7ebe1489157d4c2aaed *inst/extdata/prostate.prf
d8c9fb9d81bf243e42c2b60e4f5b3f13 *inst/scripts/data_provenance.R
6f5a048a7169c678c7b0ff5e2d57fceb *inst/scripts/raw_data/CoreGroup2Gene.txt
cdbb5afd1a6c0be41938fed4abf56cd9 *inst/scripts/raw_data/JonesS2008.txt
1c5f6c86093ac4615ee6d3874cebfa70 *inst/scripts/raw_data/ParsonsS2008.txt
ca04c412c29359f4744fa1548a31756a *inst/scripts/raw_data/README.txt
827239d0aa8b96624220389c38eef2fc *inst/scripts/raw_data/WoodS2007.txt
98cc776803bb6f625751a602a49d78d2 *inst/scripts/raw_data/cbn.py
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f56dded29fd87d9f0a9b6a711e056b5f *inst/scripts/raw_data/posetEnumerator.R
119f83c035c183c9f5cd98543173007b *man/Base2IndVec.Rd
1ebe786c88dd3022b41742dbeb21a9ed *man/Base2Indexing.Rd
76687e9231b7000574e9953e3ce1d67c *man/CBN2Path-package.Rd
9b79e59c90523b86199e71a4f6474755 *man/EdgeMarginalized.Rd
9a3e90c8a66ab8cbf819ccd9f8066ee2 *man/Predictability.Rd
805267aa0ff92e60103f95dfcf6f77f9 *man/Spock.Rd
20a0f1f370a419d9283ea2ba6f0cb465 *man/bcbn.Rd
0e79d2f783f594e872ed08564c460669 *man/ctcbn.Rd
d646379d83e957c2fc55073076d888ed *man/ctcbnSingle.Rd
dd730625fe797e4b0f98f61023eeb417 *man/generateData.Rd
a397ce34a21704e188b5019370cd49ab *man/generateMatrixGenotypes.Rd
a340351547e5898e4d5fb5fd1c0720b7 *man/generateTCGAMatrix.Rd
124f569526c38818c511ac35f1bd9331 *man/genotypeFeasibility.Rd
ce09ac94748b59535bfd03b94f5a47c3 *man/genotypeMatrixMutator.Rd
3f1d45ce767e75f9430879d5276c6c0f *man/getExamples.Rd
83605372c637e389e47721c6e78132f3 *man/getRawTCGAData.Rd
7356f904573e2a43e2f55ddbf3d8377c *man/hcbn.Rd
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20ddc65557b552132f9f0be5f7854396 *man/jensenShannonDivergence.Rd
898846d9fb8cae8a7af6cae89c1ee07d *man/pathEdgeMapper.Rd
96834e309eab559621315a33d3adab7d *man/pathNormalization.Rd
7e8046fd6480ca72bd1a257ba44e1616 *man/pathProbCBN.Rd
14532b68ec7c509d568257d996e48724 *man/pathProbQuartetBCBN.Rd
f09de2a558060ede5d01d91340354586 *man/pathProbQuartetCTCBN.Rd
dbfed10b5035a0c487a57b4265d7ff13 *man/pathProbQuartetHCBN.Rd
00b398ecb0242044062e0b3ba9dce7ab *man/pathProbQuartetRCBN.Rd
a862d927e227ed582490d3e2e56bdee7 *man/pathProbSSWM.Rd
8fbbaa440e92acd96a0ae13582e888ec *man/pathwayCompatibilityQuartet.Rd
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b9da9a1e2f674da51c6a6285128b7a3a *man/pathwayGenotypeCompatibility.Rd
3f9a3a8a77bd38dd737ae550802ba8af *man/pathwayWeightingRCBN.Rd
7b87b02c5a515ab0e9b6386eae9f86cb *man/permutations.Rd
3533b169d8270e26ce2f3bd9d86c0d4c *man/posetWeightingRCBN.Rd
25175afea8c0dce330434e6bed6963ab *man/readLambda.Rd
a4967a549d17fb301e09ed264f00ddb6 *man/readPattern.Rd
6229f8916e31dd391776be04ad3f056b *man/readPoset.Rd
80353818999b6cff01c81d9e9608da98 *man/readTime.Rd
6a80a1407a6f01948af1b4e415811d26 *man/transitiveClosure.Rd
0eae7e9cdbb6bafd587cdc0f4f3807d5 *man/visualizeCBNModel.Rd
918e35f4c20c88862511b392160522ab *man/visualizeFitnessLandscape.Rd
ff73e1590eb8e5ad5076527fed254750 *man/visualizeProbabilities.Rd
80ce2eccf0d6074acd61a55006d31301 *src/Makevars.in
228e08911007ec55d4506487671f1c5d *src/bcbn.c
57d2b0d81cee38f291276f0b3e4d5b76 *src/bcbn.h
383e78c5c32d49984e0043b780c91e65 *src/bcbn_rand.h
680b8e8e240292104f7f04c944a40c1a *src/ct-cbn.h
da2a86abc2ee50f2849b6613734429c7 *src/ctcbn.c
c9095a1dae0e3016b19ba0d46d5782b7 *src/dt_cbn.h
02c719ca813fd5bfd4b611ef815af826 *src/init.c
0638f0f762ec1980cbb453760cc8268f *src/queue.c
fa4913d6573c899ca0a1e88171bba595 *src/queue.h
abec38e92eb3fe77640ee49396010db5 *src/rand.h
63c4ea20dc55f8ebac30505e4c4602c8 *tests/testthat.R
4cef3562aeae7eeb3460e3975b4755e7 *tests/testthat/test-bcbn.R
59f330da373c43ae512451133ec13e07 *tests/testthat/test-ctcbn.R
bbd53e78b7989f410e02af403acd8fc8 *tests/testthat/test-hcbn.R
1fb560e0c0b193598c07e1e0fd33a2f2 *vignettes/CBN2Path.Rmd
