18ab2566d7d8457eb7194881340b73a8 *DESCRIPTION
d0b9be443c99ed9ab595d24d1fab007b *NAMESPACE
2c87d09a4ac05b5020a96d6b40c04bd0 *NEWS.md
d26fabc1b68717ff843355c2b17fc3ef *R/Utils.R
6620538b5fa45853dfc3f05df2896f4c *R/assignMutations.R
ba98ac44acc9a3dd9cbb1a9778fa23a7 *R/assignQuantityToMutation.R
b969dab06dee98e7b29f31efdadd2528 *R/assignQuantityToSP.R
f681553ee1461aa54733e35a518c7faf *R/buildMultiSamplePhylo.R
3874ca1872f97edcaddfc93ae8f3aaed *R/buildPhylo.R
89df549cfc6ce079c45ad7456ca84d0e *R/cellfrequency_pdf.R
3d6cd1c5583772454ce690c775d057e8 *R/clusterCellFrequencies.R
8ea4ad2a9f458f9b1a4e1cff2b4b4c55 *R/computeCellFrequencyDistributions.R
f3eb324479ae3dfb9048c8a6375d6998 *R/gatherEXPANDSoutput.R
0d72d425d2470a15fff3f72ca3c777ea *R/onLoad.R
00f60d56f26e5fc3b8bb7566dd75b15b *R/plotSPs.R
a8c1af9bbc0eb24b42fedd672cce3308 *R/runExPANdS.R
ab9b341bfd4c3b08d33af8c497bc1261 *R/sysdata.rda
45454daadee252eb81692a2ae360f267 *build/vignette.rds
664284e0624f9ce0762af69e78b0b03e *data/cbs.rda
e49b6d61d3960c03b775dc15a5b65cc9 *data/simulation.rda
6fb02c3ab0905057bf173dd43c1b8908 *data/snv.rda
8659900f7f2c5402ed5bf2a1c56209e7 *inst/doc/expands.R
c7e2810c566e550b85d667dc9ceb92e2 *inst/doc/expands.Rnw
3075eb50e74c3fd41f0e1b4613600743 *inst/doc/expands.pdf
25fa4450dc0e7c89d2c4e17a24184645 *inst/java/expands.jar
61ec5ae124d806c5b3cdbcc4b90648b0 *java/src/core/ParallelSubpopulations.java
f54454a0c5463cd1294e8458a65a93c0 *java/src/core/Subpopulation.java
db3919c3a898a8e41b9e989b7230ca06 *java/src/core/utils/AFtimesCopyNumber.java
fd76b339bb1f03075a953a4f78199bdf *java/src/core/utils/Common.java
d852f744f0c9459ee9d540617f014b86 *java/src/core/utils/CopyNumber.java
50dc18552be6982e694fda1c2f84d703 *java/src/core/utils/Measurement.java
30eeb40d35ae146e57ebc9a95f00a4f3 *java/src/core/utils/NotAValidCompositionException.java
30d4997ed255656c2b5b7dbaf3022c93 *java/uml/EXPANDS.mdzip
34e6d943306a82ee0a66f67244e6622e *java/uml/ParallelSubpopulations.tif
f671215195810e68bc98292c386efac1 *java/uml/expands2.tif
c604fd1fb6ea7a998c3561fe068f5eb1 *man/assignMutations.Rd
a7161c02c24d2a232a5995af5a895b1f *man/assignQuantityToMutation.Rd
3f75b7efa66e4c8b3c3da6cd71419a19 *man/assignQuantityToSP.Rd
7be52a8c91d376d6068b5f48dfe669c8 *man/buildMultiSamplePhylo.Rd
04c588eac64aea66fcf765a58635a316 *man/buildPhylo.Rd
182bfe9986fe62d975e0cdc4a8baf5f6 *man/cbs.Rd
df7ffe44725c9a35a596f99d558078e8 *man/cellfrequency_pdf.Rd
a09f6276e76c7e51e1c1049e25ec43e2 *man/clusterCellFrequencies.Rd
4b759085b76394a73a307558dbd16d6b *man/computeCellFrequencyDistributions.Rd
fc823a91d8ea4be7b5d8caa107070348 *man/gatherEXPANDSoutput.Rd
d184a55ed2881c0c1500407b61b6de7f *man/plotSPs.Rd
a2f8272a907692ff63f0256207acad06 *man/roi.Rd
38159b3fa0e245cb48d988eeeabc2501 *man/runExPANdS.Rd
f76ffa53859b96c2839639368c2bab08 *man/simulation.Rd
f66268438e2a944fed98e93667af49c2 *man/snv.Rd
9041422165b8dc882ccc397e3c0984d7 *vignettes/ID_MRD_001_metKidney.cbs
514b666e8d8d4bfb0f3e73f502b69e9b *vignettes/ID_MRD_001_metKidney.sps
a6611c786960fb68aee6afbfd55a5547 *vignettes/ID_MRD_001_metLung.cbs
641a5ac5f5e9ad18a8b2fca47141e3ae *vignettes/ID_MRD_001_metLung.sps
b612633a0e86597097b86fe780f6d9b9 *vignettes/ID_MRD_001_primPancreas.cbs
e0b3a168291d6ec5d752a1a23de1ca99 *vignettes/ID_MRD_001_primPancreas.sps
c7e2810c566e550b85d667dc9ceb92e2 *vignettes/expands.Rnw
291e185f5056595af2f5aa27576d8887 *vignettes/expands.bib
fa5217b6a92542a4e9f8720ab880017d *vignettes/tmp.tree
