db833a049d315033dc4abb49a1d82fef *DESCRIPTION
f0d0766890e21f1bfe3c1810a928af7f *LICENSE
3601cc7134f430ab35f8bc018375fef8 *NAMESPACE
59131dd90379a82b7f46f9a0ea322917 *R/RcppExports.R
2449f7964cdda116fdb295e9a818db97 *R/data.R
10841ff7ead3c766e34aa62bae0989e3 *R/distributions.R
bfff21f0a98aaf05d5df4addf7ef8ca6 *R/hahmmr.R
2d66b97039eb5d1751c23bb4dc2d42b9 *R/vis.R
6232da740e9c4a35f5a4c4aaa22b14a0 *R/workflows.R
889316959aa433447ac2ee173150bfb2 *README.md
2f73655087eb8953ec58c4699793e90e *data/acen_hg19.rda
3c2a0fa281beedd8f86be3a4b8858abd *data/acen_hg38.rda
8efac9c806f2810fedfb6b723fd33ae5 *data/bulk_example.rda
110fec45d03652c73294a2cb6beda054 *data/chrom_sizes_hg19.rda
8e51a671d180d287ff87861d06fa30d0 *data/chrom_sizes_hg38.rda
4f64e061bb377b655d4225d843e4535b *data/df_allele_example.rda
87d7ff149d69d09a0c05294947aba465 *data/gaps_hg19.rda
170a9ca2c3d97d0013750653d3acceab *data/gaps_hg38.rda
fcfdb2a041faf94fdd350147f338bf95 *data/gene_counts_example.rda
ecfb38f6439cdaca65e47fcc8c8cd918 *data/gtf_hg19.rda
b69826d226b2f1fffbc53a4f856210d0 *data/gtf_hg38.rda
d93edd82cb7caa0362aa2d4d1f18edf9 *data/gtf_mm10.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
5f3a25c683b2651f5dcd9600577950aa *man/acen_hg19.Rd
e1aaebd2521f61627fdad6d756b16cc0 *man/acen_hg38.Rd
63dd78ac590f8e5a5de022417f2fd1e6 *man/analyze_allele.Rd
ade4d36280ad15035353bebbc44cea08 *man/analyze_joint.Rd
028e14228e8e822c49292ab204beb960 *man/annot_cm.Rd
6fac7dacd5b7577dcf3cbc06ef724d13 *man/annot_segs.Rd
c572521a6a443d6101196eeffce0892e *man/approx_phi_post.Rd
e35fdb6319fe207bd149b95dfca8eb4e *man/approx_theta_post_s2.Rd
078dacf4776280821974e67ce4fe3f0b *man/approx_theta_post_s3.Rd
bf23b76cbdc2a3b80752ce7c8dcde11a *man/bulk_example.Rd
5eca831c9d63ac62b13e695bccf9bed5 *man/calc_allele_LLR.Rd
cd913dfd795f8048371b4ab062e73966 *man/calc_allele_lik_s2.Rd
569cb74a1440d26295b732e444deb628 *man/calc_allele_lik_s3.Rd
4e95084105428fa1ba1302a16cfb0694 *man/calc_exp_LLR.Rd
3b8ae9d0d8210c62bf38418f5b59fce8 *man/calc_trans_mat_s15.Rd
c2a82a664d39ed3fb90c0f37cb266c4a *man/calc_trans_mat_s7.Rd
33f50593b2d8de794f3755769cb306b2 *man/check_cols.Rd
1ab1b6f034416df0bb7f9c209e7b49bc *man/check_matrix.Rd
f58158f8b8f9b55a66d75e179719ecf2 *man/chrom_sizes_hg19.Rd
a3802a643cf910e9f519993c24a946e8 *man/chrom_sizes_hg38.Rd
7c82eb6989fcc946463eaf78d94d2f51 *man/classify_alleles.Rd
56ff33d4e5b47cb702400de5294da898 *man/combine_bulk.Rd
8bddbea37ea6a1861cbeda88eb825e21 *man/dbbinom.Rd
5f69bf0805355adc5b693103b1445702 *man/df_allele_example.Rd
e331fdf2690263bbb253c7c5f218dcdf *man/dpoilog.Rd
11f36c36da636341c755a40aa3139fcd *man/filter_genes.Rd
4aff62efea703cd30169d7f7e7609a25 *man/fit_gamma.Rd
693f220d76ad320b21d5b6f129ba2f8d *man/fit_lnpois_cpp.Rd
46fee729636ceabb1e46e03b7e83a0ad *man/fit_ref_sse.Rd
a5ed43b98552469a90dfd7ef42f3d63d *man/forward_back_allele.Rd
65b6cc6ea6ac371e57b682b9c6f2971b *man/gaps_hg19.Rd
21f5bfa157622ce2a12840e185de296c *man/gaps_hg38.Rd
fbe34319e0023fc535970f8f882f3561 *man/gene_counts_example.Rd
24f9bec990c28e07d08abafea1b541e9 *man/generate_postfix.Rd
a2d8a921d768d6c6b65cf4b421a3c198 *man/get_allele_bulk.Rd
0bd6ef987ab0a84aaa4ae64eab908163 *man/get_allele_hmm_s2.Rd
07eb8c2e2de3377a74ebd05fcd794e4f *man/get_allele_hmm_s3.Rd
e172d982b321f13b5ee67710677bf01d *man/get_bulk.Rd
d28beaa581276b151af8d8e0a0a4921d *man/get_exp_bulk.Rd
16f7516da08ed469d2932546dfee6d29 *man/get_trans_probs_s15.Rd
d120247f04a8cadfff1814e246425fc8 *man/get_trans_probs_s7.Rd
f5dfe96e32940270a7e65b811d900a59 *man/gtf_hg19.Rd
6a9528eed118256a5e42d3480d50fb78 *man/gtf_hg38.Rd
9a04926616cf1511ceedc5740c4ad9b3 *man/gtf_mm10.Rd
f2d49475376b9e8113215304551bdb2b *man/l_bbinom.Rd
4012749a0b8ee767800488129ede8af8 *man/l_lnpois.Rd
a4d3a90966c9c1805a82a315e189d895 *man/likelihood_allele.Rd
9fd2f49a75d2b0fddbc35aee5aeb6253 *man/logSumExp.Rd
576c8f6fc9c5c41aacc1efb80d234121 *man/plot_bulks.Rd
0a95f6bf87c87095cafda42450daf72f *man/plot_psbulk.Rd
9d40b069baca47035ea22845e08e2c58 *man/pre_likelihood_hmm.Rd
4141230e3c1a8b05fed58e59042943f9 *man/ref_hca.Rd
9a6d4eb5bf60efe8dbe0bf956cd3afac *man/ref_hca_counts.Rd
75afb35d7348c09ec4b034f3ac944a7d *man/run_allele_hmm_s3.Rd
86cdbe04fa98aff69e6c373b447d3d6d *man/run_allele_hmm_s5.Rd
16d103c24c1dabdf9bded5e8ead10c7d *man/run_joint_hmm_s15.Rd
a80566b3f0578a425e2fecd1902e38b5 *man/run_joint_hmm_s7.Rd
d13af4aed9049727a81db474c692ad0b *man/segs_example.Rd
3da1358b521a038ef5d0b25688a1f8a0 *man/smooth_segs.Rd
4ebd860080a5166b08940851b862663d *man/switch_prob_cm.Rd
e3885c67d44b99a62da639827593147c *man/theta_hat_seg.Rd
36eae748d6ab493555c6ee7e60c143c1 *man/vcf_meta.Rd
cae195fee8a99bfa29fc980035db1464 *man/viterbi_allele.Rd
2439ac1c03c1ab966a111f70a4e62035 *man/viterbi_joint.Rd
f67bdd046b06597eccb3f548f7570518 *man/viterbi_joint_mat.Rd
019f6c90a9c24178f9ebeaa3b94809f6 *src/Makevars
3241f7543f2203fa0b7ffa4fb5b1b847 *src/Makevars.win
bea6881a83764a1347f8d16965d4c54d *src/RcppExports.cpp
55acc414721e74c9b7b0fc4cdbad452f *src/bbinom.cpp
ba558973dd0fe543c0be8f2e214ef2d9 *src/hmm.cpp
d6b9e9547ce5720fcd90d5fb19b387ee *src/misc.cpp
cbcbc4f2d94c6560dc120a72fc47bf87 *src/mle.cpp
aafdd91c9a912bd003a596e1bc983517 *src/poilog.cpp
bb2d0d6c979f390842487e95b0e7540b *tests/testthat.R
d679f085b9d099db4cb4fb5e5d1e4048 *tests/testthat/test_functions.R
