3ce83fecbf2510a1e9561361443b9161 *DESCRIPTION
e53055fb04387935dc54d88754ded6da *LICENSE
9f925e827fbf3e37bf8e59124932ac34 *NAMESPACE
e3406c32934b75d6da6fce0ce47eb190 *NEWS.md
8d1499b61fde3681fc52c87256e83bc1 *R/RcppExports.R
3d9032f0c7346cda8c018243e4394460 *R/class.R
eecb2d57439ae3567c7f58f89b9ca6f8 *R/data.R
83e2556e88680f198380ae591fa76e6f *R/diagnostics.R
94e0b43b8bca25a7991c8a36296b4999 *R/genotyping.R
2c56dd13255b25653f1fabba96340299 *R/hmm.R
a8d7a04e096658841a63b47eb43013bf *R/main.R
c6bda899fcd4af5d03456bbd6a30ecfd *R/poilog.R
069f72267692610220ab1bd96dae1ae0 *R/trees.R
3ef23a7006eba2ee879ba50e94bc6b86 *R/utils.R
5196257e5af1da8431ed39ac5f8978e8 *R/vis.R
03fbda888349616c7a8ae8c57d03da6a *R/zzz.R
82982a2a24f367ab80833b9be385ebd6 *README.md
2f73655087eb8953ec58c4699793e90e *data/acen_hg19.rda
3c2a0fa281beedd8f86be3a4b8858abd *data/acen_hg38.rda
d10c40d5a6f52be081ea1503011c5ee5 *data/annot_ref.rda
3c44a7122ecc7c37340064346810f00e *data/bulk_example.rda
110fec45d03652c73294a2cb6beda054 *data/chrom_sizes_hg19.rda
8e51a671d180d287ff87861d06fa30d0 *data/chrom_sizes_hg38.rda
da5f54890115872f9913b942a9860942 *data/count_mat_example.rda
5109b7b39bde341c27f8e19ee79f9ece *data/count_mat_ref.rda
090c07e49539446ce3f1becceffecd16 *data/df_allele_example.rda
87d7ff149d69d09a0c05294947aba465 *data/gaps_hg19.rda
170a9ca2c3d97d0013750653d3acceab *data/gaps_hg38.rda
8056489bed391bbfed49822f75e9dc65 *data/gexp_roll_example.rda
ecfb38f6439cdaca65e47fcc8c8cd918 *data/gtf_hg19.rda
b69826d226b2f1fffbc53a4f856210d0 *data/gtf_hg38.rda
d93edd82cb7caa0362aa2d4d1f18edf9 *data/gtf_mm10.rda
09d277ba1b9eb86796aea100cc8020bd *data/hc_example.rda
0751f87c967a6d96c889cc0b7c0be39e *data/joint_post_example.rda
18941cefa9dd01fbf8eb457899bdeb51 *data/mut_graph_example.rda
7491738d49b04b63b3abed202502cac5 *data/phylogeny_example.rda
785979e12c8c49b6445658bd70658cc0 *data/pre_likelihood_hmm.rda
321cabe1f8208be8ef07f9823360b9c7 *data/ref_hca.rda
6b62eb0bd388965e2948c654b1915ceb *data/ref_hca_counts.rda
ab0d33f7f58ac0e78bc0d84fde8a54ad *data/segs_example.rda
8629d8aa8c7de2379b796e44d4e518d2 *data/vcf_meta.rda
a1bff53e63bd626825ac4e9ae571af5c *inst/CITATION
6c6560abbde89bddb8f507cd2c4a9fd7 *inst/bin/pileup_and_phase.R
a70bba6c305768196164826dae09fb63 *man/Modes.Rd
b93f7030c1167fa34df05324a8c69da0 *man/Numbat.Rd
5f3a25c683b2651f5dcd9600577950aa *man/acen_hg19.Rd
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57c734a865b54e94703d4bda2f091d52 *man/aggregate_counts.Rd
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7dec7026d1ae524a043b039c14afb44f *man/annot_haplo_segs.Rd
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d768963335fa99905ffe5087577975ad *man/annot_theta_roll.Rd
fdc81516a52ce56235b7324c68fc6200 *man/annotate_genes.Rd
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57c822a93d4f0dafcef1c7b7938bdeb3 *man/approx_theta_post.Rd
83e1883f8e25f3190a03fae91b2febd5 *man/binary_entropy.Rd
4c646c9523b918920c7cc6504ae5decd *man/bulk_example.Rd
3dd1be23d6445784033e4160716398fa *man/calc_allele_LLR.Rd
834d5b776f972dec676d4997fedc1134 *man/calc_allele_lik.Rd
a8f1fe25d4b5c6e2fbc021356f310e1d *man/calc_cluster_dist.Rd
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58f4016d7c029b12daf048f59bb8ad29 *man/calc_phi_mle_lnpois.Rd
9f184f6f2fee9a7130966b9b619d3727 *man/calc_trans_mat.Rd
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de612602a62aa7aac4d6955a951bf987 *man/check_exp_ref.Rd
69c721d6e6fe930721968a3b74287d74 *man/check_matrix.Rd
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a3802a643cf910e9f519993c24a946e8 *man/chrom_sizes_hg38.Rd
647d7653d2d96788dc5b852ac27164cf *man/classify_alleles.Rd
a8012559101c6143c4a38982720e028f *man/cnv_heatmap.Rd
97fc57865cd38b237ef0163655bb7dee *man/combine_bulk.Rd
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eecfbb7b18e261a7cd20d6877a989e12 *man/count_mat_ref.Rd
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a764755bd52d2ab81339763e2ce48175 *man/detect_clonal_loh.Rd
96b13c14b0535c0259c9be3aa22e8c3f *man/df_allele_example.Rd
c565d6cd980451367229a7757b034668 *man/dpoilog.Rd
d64eb84839adf8dc2822c5270f3e9bcd *man/exp_hclust.Rd
c92afb312e4edea2257fca1d3d425043 *man/expand_states.Rd
1869d9978dbf46fdacb24889a938e6ea *man/fill_neu_segs.Rd
eb3262a9d70e8297fd79189e49c7c77e *man/filter_genes.Rd
906d99a1bddd7505fb0028a91d3e1d4b *man/find_common_diploid.Rd
a73b952a50e53d225de493e30093f73e *man/fit_bbinom.Rd
14f14bc1807f79622bea0f5d793e3dec *man/fit_gamma.Rd
6261d771ff773221e36b778188b89896 *man/fit_gpois.Rd
ab0ad31eaa1a1adc446c9aa4efe2d8f2 *man/fit_lnpois.Rd
e8f19cb0c772846795db648fdc3fe6f1 *man/fit_ref_sse.Rd
42dec0dee677eb48d0a8f6d311979777 *man/forward_back_allele.Rd
65b6cc6ea6ac371e57b682b9c6f2971b *man/gaps_hg19.Rd
21f5bfa157622ce2a12840e185de296c *man/gaps_hg38.Rd
3be2612c63806c8f3acb7625ba7dd741 *man/genotype.Rd
b6b25cae4904cb6cff071131c5754497 *man/get_allele_bulk.Rd
227674ae5ed58270e541296be5ef866c *man/get_allele_hmm.Rd
fdb613088b0aba6007896470db9df2db *man/get_allele_post.Rd
a505bda56ccfaac36407dcf1c2549386 *man/get_bulk.Rd
233d1decd8a98b8a182fae8ac90d15e6 *man/get_clone_post.Rd
238d8ada41780c2129c7499b7cb7e1de *man/get_exp_bulk.Rd
9ee46ba89f00d0657cc91f46b53493b5 *man/get_exp_likelihoods.Rd
3402e7e652b373cc4062880082c91d60 *man/get_exp_post.Rd
b5fbd2d6e2a1214e3b74d8c9f499014b *man/get_exp_sc.Rd
309c13014738a09e98f2abd780d17dc1 *man/get_gtree.Rd
765603ee6e548d6e82cba36dc235b418 *man/get_haplotype_post.Rd
9e86e996bec560cd6d109f0548224e21 *man/get_inter_cm.Rd
a032c4e9685f17fb9b8053d35d5e87a4 *man/get_internal_nodes.Rd
d99df8bcce08ed4e27ed9ff6e361633a *man/get_joint_post.Rd
af920895d72f34e5b4399349186f7dd2 *man/get_lambdas_bar.Rd
708e0b272ad529b84c262dd39c075154 *man/get_move_cost.Rd
12885c5d727456834d76ec7f51afa535 *man/get_move_opt.Rd
fcb2f94e13cdd0ed6a56010a198dbb50 *man/get_nodes_celltree.Rd
6ac75bc26035e5686388398500c81782 *man/get_ordered_tips.Rd
82eadd101cc1371432dfbc19278468ce *man/get_segs_consensus.Rd
6f036508d4b6cdb4630bfc5e54a9b7be *man/get_segs_neu.Rd
0db28857d8f80414ae76a118629ea7b2 *man/get_snps.Rd
089fc3814c9164bd8fcf7071122c4681 *man/get_trans_probs.Rd
6c555d4ba2c493a723643fd723b5cf4e *man/get_tree_post.Rd
573a13ade55d5ffa9651c9cb47ecdbb2 *man/gexp_roll_example.Rd
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6a9528eed118256a5e42d3480d50fb78 *man/gtf_hg38.Rd
9a04926616cf1511ceedc5740c4ad9b3 *man/gtf_mm10.Rd
7bb0fb3e8505bc26a93ebc4b7f0dead6 *man/hc_example.Rd
2d43c4c24c8420be8cd33ddf25e93d76 *man/joint_post_example.Rd
e9d196a7cac3366ddcba5352f9a44e64 *man/l_bbinom.Rd
d55961078848716109969e5f1384b6a3 *man/l_gpois.Rd
d7245fd75378cf8f6a4dc4bdd9859592 *man/l_lnpois.Rd
6ee7c95640d8b121dc8d2373f2efc472 *man/label_edges.Rd
abfa00a6cdac1de7d2ac029601029e06 *man/label_genotype.Rd
651dd9af834483350b77f82fc12b964c *man/make_group_bulks.Rd
3171404944cc383a5882e1fe1adb424f *man/mark_tumor_lineage.Rd
961358a199dc673f256ce56ccb5507a1 *man/mut_graph_example.Rd
d6c2e46de59e333c251e70686e85b9a6 *man/phi_hat_roll.Rd
0ba0f48782645406944d590fca17c88d *man/phi_hat_seg.Rd
979819234d1f5b1c6a0a1088e6485b6f *man/phylogeny_example.Rd
576c8f6fc9c5c41aacc1efb80d234121 *man/plot_bulks.Rd
765032a0e20733d099e7a048e2a17a19 *man/plot_consensus.Rd
e2997ae04cb14dff48f01e2cca05bfba *man/plot_exp_roll.Rd
234fb5d28b4cee2619247f34943ff724 *man/plot_mut_history.Rd
2b7b4e01b88794b190cf27986cbe0156 *man/plot_phylo_heatmap.Rd
0a95f6bf87c87095cafda42450daf72f *man/plot_psbulk.Rd
86c23706f25bad078be510a67ba64fc8 *man/plot_sc_tree.Rd
e591ec7b54861a6dbf12d69e8b9dcea3 *man/pnorm.range.log.Rd
9d40b069baca47035ea22845e08e2c58 *man/pre_likelihood_hmm.Rd
80f21c8b7982ea6ea48355bc28f012bc *man/preprocess_allele.Rd
4141230e3c1a8b05fed58e59042943f9 *man/ref_hca.Rd
9a6d4eb5bf60efe8dbe0bf956cd3afac *man/ref_hca_counts.Rd
5d7b72ba3592d32a97f58a47cf363cad *man/resolve_cnvs.Rd
4e9bfcf999516dd3966894188dd8ec87 *man/retest_bulks.Rd
5c34697ebc441a649d524d75f709af8f *man/retest_cnv.Rd
a5de9616caa726309a2e62e1efc00ed2 *man/run_allele_hmm.Rd
19d883a9517325212769b80702691745 *man/run_group_hmms.Rd
4cad98a7dfb43f392cd21a4823933260 *man/run_joint_hmm.Rd
d82c6871742020c9b03e064623c892ff *man/run_numbat.Rd
d13af4aed9049727a81db474c692ad0b *man/segs_example.Rd
1166f1e935b0f4d84f80c8befbe95736 *man/simes_p.Rd
3cfefefda66f5f4fbf438266434132b3 *man/simplify_history.Rd
688a8f5b2ba1ee7dd4e7ce8e54119a13 *man/smooth_expression.Rd
42a8f8c61edc5c87d13bfa0bef485c75 *man/smooth_segs.Rd
d732c7e9bed62eb964eeaf89df9a3ec9 *man/switch_prob_cm.Rd
f78da2eba888ebc83f6153deb1c7a099 *man/t.test.pval.Rd
c379d9c17346843cdc1bd2239cea1f69 *man/test_multi_allelic.Rd
aa7f09d1c3a8aac26390e5d9fe463e5e *man/theta_hat_roll.Rd
8df67c3e8a75124329b76dda82188af7 *man/theta_hat_seg.Rd
20175bdc0cc66a43a7192b77d9925507 *man/transfer_links.Rd
ad7d9266f3710a7f0472ac0c3c390174 *man/upgma.Rd
36eae748d6ab493555c6ee7e60c143c1 *man/vcf_meta.Rd
ac6559ff06c8672d4073b2014a1d649d *man/viterbi_allele.Rd
816d09a90c8782ac4b55ab54caf40431 *man/viterbi_joint.Rd
c0635e97ffe815c43f338b7b90598b21 *man/viterbi_loh.Rd
e90c1b32e302845a3a47eaa95b39c9d1 *src/Makevars
8dc931b61237b026d4167c6750ef1165 *src/Makevars.win
ebecec29a657fea22411a2f84b7bfa3f *src/RcppExports.cpp
55acc414721e74c9b7b0fc4cdbad452f *src/bbinom.cpp
c10d24313504ab951b01089f5689f7f1 *src/hmm.cpp
d6b9e9547ce5720fcd90d5fb19b387ee *src/misc.cpp
3f9bcc6d5c04d1dce72588e3ef3c7381 *src/mle.cpp
aafdd91c9a912bd003a596e1bc983517 *src/poilog.cpp
2f1b082304a8cbe8df9855da2c4112dc *tests/testthat.R
c914b21dd2e7f1b51ab51da28e6e838f *tests/testthat/test_functions.R
