c7098b5b23fbc23337111df2e5baba33 *DESCRIPTION
db1682e19ef2223eeaaf428756df6e02 *NAMESPACE
f2283b65a71fe786a5a8fa81c238ee23 *NEWS
a350b33edf324af36dc9e0a5f77a59d8 *R/bam_functions.R
08c58cf576302f8fafeaafd66b03b5d3 *R/classes.R
73aa737f94b73147a7c84e502c09fe99 *R/clustering.R
29f3936c01b47740a6d861fddf318598 *R/data.R
5b6ddba6e73c592253ee59120bde8818 *R/functions_tree.R
9e2a36393902d7b3fb9a99c727fcb2d0 *R/mutationCalling.R
ca9a4e64cb9c3553de32c88395a91eba *R/sysdata.rda
00d3160b89d3bed38082613e56967fae *R/vireo.R
9fd8f027b23f12a39f0bb40160cf4da7 *README.md
0ab01eb8b7c7863241fb309c555c0a1d *build/vignette.rds
94de6eede0bb3d09b555d715a6320291 *data/M_P1.RData
2ab3339a8be7a48ab1c39b147938b62e *data/M_P2.RData
47bc44afea9033a4ff5537ea6cdcbc70 *data/N_P1.RData
ca5a52c762e93455122542fb0812e45f *data/N_P2.RData
8c8d39b5da4283ed9ec73b1f7b15f3e4 *inst/CITATION
1c453e7d35264b67e77f4cfbfb1dccb2 *inst/SCITEpkg/README.md
441da25a084dc0251f1c71675052160a *inst/SCITEpkg/findBestTrees.cpp
24cc744163f05f56eb5c056754e016e2 *inst/SCITEpkg/matrices.cpp
0c30d07b4f2f505c9f2873296b68b464 *inst/SCITEpkg/matrices.h
d9d3175fc3bcac7e74b8a775d72605be *inst/SCITEpkg/mcmc.cpp
9722937e05c7a47bb4fc035113ec7e00 *inst/SCITEpkg/mcmc.h
aa6bd10f34c6ca1d46c035e9bd523846 *inst/SCITEpkg/mcmcBinTreeMove.cpp
92ed03d607076f8351ad238a4923e793 *inst/SCITEpkg/mcmcBinTreeMove.h
187a3dc0b50d8d6d69a5798c8dad9a38 *inst/SCITEpkg/mcmcTreeMove.cpp
02bfa00af6681e80acdd0d9e8d6a5997 *inst/SCITEpkg/mcmcTreeMove.h
7da0281fff2e656e2fd1a97190877954 *inst/SCITEpkg/output.cpp
2a487f9f13aacf18a6c10d5a68636348 *inst/SCITEpkg/output.h
dae220a9427605c41d829adff55626a5 *inst/SCITEpkg/rand.cpp
f7977efec0569ea7072ebd94edf710b8 *inst/SCITEpkg/rand.h
274d3abd011a24aeae0f02838342c4e0 *inst/SCITEpkg/scoreBinTree.cpp
d5c0fd453c381819d746d04a2e2728b4 *inst/SCITEpkg/scoreBinTree.h
ab9d37be1f979babcc809c9c0017ab0f *inst/SCITEpkg/scoreTree.cpp
6be789db89746497db22d86d1c1bd594 *inst/SCITEpkg/scoreTree.h
fb3efad6b02e95889357e3903575c4b3 *inst/SCITEpkg/treelist.cpp
6e55d843ff04d914068c3141c06268b4 *inst/SCITEpkg/treelist.h
b0002b1dbf2f2e07e8fa19de18900a35 *inst/SCITEpkg/trees.cpp
60d016269ce68fdccdd1b3e41e702717 *inst/SCITEpkg/trees.h
8a3a2f34ade205341bc549e64d4b5bea *inst/doc/clustering.R
79c0200f3e458ba81b6c16c0f78d8961 *inst/doc/clustering.Rmd
00550d262c4093194606c0b4ab58f74d *inst/doc/clustering.html
a8243374423b75804232cae158b94feb *inst/doc/overview.R
47e3b0300fc6960620925f505085b9fa *inst/doc/overview.Rmd
b32c4c6ffe172d1ede7df703aff77348 *inst/doc/overview.html
29309a44ca1933f79ff6b197c3b677e6 *inst/extdata/LudwigFig7.Rda
b8d2e5034b419ff6463937846aa1340b *inst/extdata/example_counts.Rda
08e89c9f01505ff6184a275e21b6ca1c *inst/extdata/mm10_10x.bam
15c920cc46edc7d2f16b609e7db26a48 *inst/extdata/mm10_10x.bam.bai
583c9140a54366ac9120090fa8c0667f *inst/extdata/sample_example1.RDS
e99b3cf183e3d2a72c813c2b639ea583 *inst/script/README
1aa5875e40553e6b07741abc61265d9a *man/bam2R_10x.Rd
01e8f2e8a090c1b5de8edb959ff1a791 *man/baseCountsFromBamList.Rd
68dc8d0ba24e9dd1999e16ca6e25b10a *man/clusterMetaclones.Rd
88fb5c7c27ddb4a72ae4822f1c88ac09 *man/data.Rd
2677d635d9e1b8086bdb5c34bf4beb56 *man/figures/logo.png
15f249a326dce7d4946a00543aee38c6 *man/getAlleleCount.Rd
9b6720edf254846dfc4d8037c69ad4e3 *man/getCloneLikelihood.Rd
7fecbc11893b30bd0f38f332aadcfddb *man/getVarsCandidate.Rd
4cebd9b834222915a446f262d481fca0 *man/mitoPlot.Rd
633811c494da8e9da85e4759c062ba73 *man/mut2GR.Rd
e9e2390b222a96141f74633a34576891 *man/mutationCalls-class.Rd
3b4dead6504a95f82816ef0fd27bdbd3 *man/mutationCallsFromCohort.Rd
7fa1c08e954abca1040138167549bf7d *man/mutationCallsFromExclusionlist.Rd
72717bb3679842cc65fe406b6dfcfe28 *man/mutationCallsFromMatrix.Rd
47680e1864da7584c6a025f9216ff2aa *man/overwriteMetaclones.Rd
198c2b391ec405a498d8a42401d8799f *man/plotClones.Rd
84147c76661ed4a377106c47520a02c7 *man/predictCellAssignment.Rd
94fb8a15585515bbadc7ad1751c7d90d *man/pullcountsVars.Rd
c69fe56c30c188e32347498ad241b66d *man/quick_cluster.Rd
4ec0765183fd870e9dcec05fe89f1f63 *man/removeWindow.Rd
ec20b7da191ca7ebd8391548b422027b *man/setVarsCandidate.Rd
347706bb0c6fdd9b5504573113cccd80 *man/varCluster.Rd
b12a3f038275a9f0343414c75aa4f088 *man/vireo.Rd
3696a7151d2a6a6fef5d9265facbd8fa *man/vireoFit.Rd
9526be7eb0bbde655cefc12ec43eb693 *src/Makevars
fb6567a2a43b2881d97ef53827953989 *src/bam2R_10x.cpp
081598a3dd2d63a8f8ef2df4f274bee1 *tests/testthat.R
5a3889fd07640dbd3ca69d5c65c4948b *tests/testthat/test-bam.R
79c0200f3e458ba81b6c16c0f78d8961 *vignettes/clustering.Rmd
47e3b0300fc6960620925f505085b9fa *vignettes/overview.Rmd
