117a2a2aacc164c15788e3023ebca540 *DESCRIPTION
e53055fb04387935dc54d88754ded6da *LICENSE
63ff7bf0da71b88eecd7798626df0bb4 *NAMESPACE
7779daddff869048ed579c4cbfc91cd2 *NEWS.md
2fa8e5d744d470feccf347be073e9f54 *R/RcppExports.R
a0f1ee4e2ab6dda3d6c171c5c243f5ae *R/class.R
eecb2d57439ae3567c7f58f89b9ca6f8 *R/data.R
39439d11e6b0a96e08841c09b7895f32 *R/diagnostics.R
256229d4f8abdb8f3be80038e0c5e363 *R/genotyping.R
65b4121f4202b9825f7836c1be441406 *R/hmm.R
d5fa8bd80b06a442a899087d42a673f2 *R/main.R
35acf11c56971fe3bacd8cff4d527f64 *R/trees.R
dd21c14cb9e5662baba9bc40bf6248a9 *R/utils.R
3776ccbcd36b9a68e84a8af079fa69ec *R/vis.R
03fbda888349616c7a8ae8c57d03da6a *R/zzz.R
91392da7897ffa11775bb1aa650f3606 *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
3caad4e4f811652b499c880e802779bf *data/mut_graph_example.rda
1917df1ef5916159f754c228833d75a9 *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
67d5a927a305aa42d785b65865286698 *inst/bin/pileup_and_phase.R
a70bba6c305768196164826dae09fb63 *man/Modes.Rd
d2aae7223b83710b35652b8cdeadf3aa *man/Numbat.Rd
5f3a25c683b2651f5dcd9600577950aa *man/acen_hg19.Rd
e1aaebd2521f61627fdad6d756b16cc0 *man/acen_hg38.Rd
57c734a865b54e94703d4bda2f091d52 *man/aggregate_counts.Rd
b16491773d2663dedab6aee03565ee74 *man/analyze_bulk.Rd
d4c5c4b6907435ed7f5dac0f1b630056 *man/annot_consensus.Rd
7dec7026d1ae524a043b039c14afb44f *man/annot_haplo_segs.Rd
2b0648d9dd96b76114ed1622ad8433ce *man/annot_ref.Rd
e2d5e3e68a2e8d8dcc3c0e3a90c69499 *man/annot_segs.Rd
38d70c3fea894f34a196b31805405c30 *man/annot_theta_mle.Rd
d768963335fa99905ffe5087577975ad *man/annot_theta_roll.Rd
fdc81516a52ce56235b7324c68fc6200 *man/annotate_genes.Rd
88049f89ea66c88234b320371ab43ca7 *man/approx_phi_post.Rd
6311f9b827d9c807fd3f0e84f380c0f6 *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
2be769edb51046a0728c10263e6f60e7 *man/calc_exp_LLR.Rd
58f4016d7c029b12daf048f59bb8ad29 *man/calc_phi_mle_lnpois.Rd
81bb1f763c4a75dc1ca676d0ad16f894 *man/check_allele_df.Rd
df26e7b341de95137958031b7276a0da *man/check_contam.Rd
68bfb0f4be3f9bb20e0093eb1e9a3dd5 *man/check_exp_noise.Rd
4393cf2213458eb6f66dc7c09565f0c1 *man/check_exp_ref.Rd
f0fcad7d97a7e7ca64f1f8d353e698ea *man/check_matrix.Rd
0d85139c79db7fa81cbbd53db895de9f *man/check_segs_fix.Rd
e623a99cf402f4f1c92eb1cc78cdf208 *man/check_segs_loh.Rd
1834e3bd1775e539edfd49d6f7428c05 *man/choose_ref_cor.Rd
f58158f8b8f9b55a66d75e179719ecf2 *man/chrom_sizes_hg19.Rd
a3802a643cf910e9f519993c24a946e8 *man/chrom_sizes_hg38.Rd
647d7653d2d96788dc5b852ac27164cf *man/classify_alleles.Rd
a8012559101c6143c4a38982720e028f *man/cnv_heatmap.Rd
97fc57865cd38b237ef0163655bb7dee *man/combine_bulk.Rd
540cf1295c2508b21d032f522d6c8e02 *man/compute_posterior.Rd
33454b891a327e6d5c336cef9368f0f7 *man/contract_nodes.Rd
9d40cad2027f873c6a5f94a6144ae938 *man/count_mat_example.Rd
eecfbb7b18e261a7cd20d6877a989e12 *man/count_mat_ref.Rd
c52b25db1c95e7105c297702d69c9966 *man/detect_clonal_loh.Rd
96b13c14b0535c0259c9be3aa22e8c3f *man/df_allele_example.Rd
fd5753e357c9415e2ef233858d2ce017 *man/exp_hclust.Rd
c92afb312e4edea2257fca1d3d425043 *man/expand_states.Rd
1869d9978dbf46fdacb24889a938e6ea *man/fill_neu_segs.Rd
eb3262a9d70e8297fd79189e49c7c77e *man/filter_genes.Rd
cfc6383dfaa7b45ebda5598eb126d7db *man/find_common_diploid.Rd
a73b952a50e53d225de493e30093f73e *man/fit_bbinom.Rd
14f14bc1807f79622bea0f5d793e3dec *man/fit_gamma.Rd
ab0ad31eaa1a1adc446c9aa4efe2d8f2 *man/fit_lnpois.Rd
e8f19cb0c772846795db648fdc3fe6f1 *man/fit_ref_sse.Rd
34813cf5a43015ee6f47dedfddbbc14a *man/fit_snp_rate.Rd
65b6cc6ea6ac371e57b682b9c6f2971b *man/gaps_hg19.Rd
21f5bfa157622ce2a12840e185de296c *man/gaps_hg38.Rd
3ef3ecf6afccf3898c400b5218de8cd6 *man/generate_postfix.Rd
3be2612c63806c8f3acb7625ba7dd741 *man/genotype.Rd
b6b25cae4904cb6cff071131c5754497 *man/get_allele_bulk.Rd
227674ae5ed58270e541296be5ef866c *man/get_allele_hmm.Rd
fdb613088b0aba6007896470db9df2db *man/get_allele_post.Rd
df10011eef4f6c3dd7576a5b47b85e39 *man/get_bulk.Rd
233d1decd8a98b8a182fae8ac90d15e6 *man/get_clone_post.Rd
238d8ada41780c2129c7499b7cb7e1de *man/get_exp_bulk.Rd
66a115d2860542ce853202662cb35bbf *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
c7d188e378af3bdafdd8c15212a50255 *man/get_internal_nodes.Rd
d99df8bcce08ed4e27ed9ff6e361633a *man/get_joint_post.Rd
9fa12c8057f2007ced4c11b9d3696760 *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
6c555d4ba2c493a723643fd723b5cf4e *man/get_tree_post.Rd
573a13ade55d5ffa9651c9cb47ecdbb2 *man/gexp_roll_example.Rd
f5dfe96e32940270a7e65b811d900a59 *man/gtf_hg19.Rd
6a9528eed118256a5e42d3480d50fb78 *man/gtf_hg38.Rd
9a04926616cf1511ceedc5740c4ad9b3 *man/gtf_mm10.Rd
7bb0fb3e8505bc26a93ebc4b7f0dead6 *man/hc_example.Rd
2d43c4c24c8420be8cd33ddf25e93d76 *man/joint_post_example.Rd
6ee7c95640d8b121dc8d2373f2efc472 *man/label_edges.Rd
abfa00a6cdac1de7d2ac029601029e06 *man/label_genotype.Rd
0074de5a614ae1dfb9f4216004eb06f8 *man/log_mem.Rd
dc764692cfda4b1f78ea4de7ca6bc9fe *man/log_message.Rd
1da9a774b6d20eaa7183112087afa66d *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
1cd82c1bcbdf7e70079eaa6d4e77381e *man/relevel_chrom.Rd
5d7b72ba3592d32a97f58a47cf363cad *man/resolve_cnvs.Rd
afd8f1f662ea65457cea7c4c204a0b26 *man/retest_bulks.Rd
5c34697ebc441a649d524d75f709af8f *man/retest_cnv.Rd
7df7ea82e4d11034e32b83f8a059df3f *man/return_missing_columns.Rd
7a3283c511a9e1e477c26cdf2b303600 *man/run_group_hmms.Rd
a15dc24bc18a1fa404806192fa8a8cc6 *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
dcdb097ff7db28712b5abdf849a56484 *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
64722447ea80971354ef9e9ec0e1a87e *man/viterbi_loh.Rd
d84ce45f027263dc4159f550cd5fb5b6 *src/Makevars
a23ffe8c6afc95b0dacc3f89b42eef4b *src/Makevars.win
1175a5d161b78095a92e8d294434d455 *src/RcppExports.cpp
d6b9e9547ce5720fcd90d5fb19b387ee *src/misc.cpp
2f1b082304a8cbe8df9855da2c4112dc *tests/testthat.R
70d1e3784019c5af64c493aef306695c *tests/testthat/test_functions.R
