36664004250f1d5cf6488678d75997e2 *DESCRIPTION
48e8269402770627700c0d903806204d *LICENSE.md
d3e9bd88ee3d539575659c61b55e3800 *NAMESPACE
2900fd99026a271d7402396ef52cc105 *NEWS.md
7778d73ad197e05967d2d4f1804f4e4f *R/LACHESIS.R
a5fd74f34d4a63cf328aa864c6732bc3 *R/MRCA.R
ba4dd0ad038ba76e09a5718121386f81 *R/clonalMutationCounter.R
a3b7040d8f449830c12932a5d0df3f60 *R/estimateClonality.R
b0c5fc3c5a045404976d0884b86b56df *R/nbImport.R
0b76b768b95008d1cc69c962ac201bbc *R/normalizeCounts.R
8f6567ffd159787e99fea028043d2f6e *R/plotClinicalCorrelations.R
9b2bd7dc6517e57b419f2372f42a6a15 *R/plotDiseaseTrajectories.R
8fb575383b97ccac621a8e6bb4b6484a *R/plotMutationDensities.R
5661ad5751b936be13399661a049cc3e *R/plotSurvival.R
8602e0dce676182b90a8a6f0d2d02b6f *R/plotVAF.R
88c6c1621630e02b1c397143e05362ca *R/readCNV.R
380ae47582c830e400abe909bc6de705 *R/readVCF.R
d19bce3983caa79757eddae019980093 *README.md
4d7ba934c9f147aa7bb9895bb60d3465 *build/vignette.rds
ece5aa136bbe070b522d7a81b4e1fcb9 *inst/CITATION
4b78fb793f25efd33163426b97a4e1e3 *inst/doc/vignette_LACHESIS.R
2818e632df1c7c1b17db31c304c890dc *inst/doc/vignette_LACHESIS.Rmd
ca491738c0a5c83d0251c10a1077a733 *inst/doc/vignette_LACHESIS.html
94d2629d85dd4ad90b5186bc2a9f8f04 *inst/extdata/ACESeq/NBE11_comb_pro_extra2.59_0.83.txt
8b994519d2411f18b60adfd26acbf89b *inst/extdata/ASCAT/S98.segments.txt
898b737c1e9a6cf972c4121d937d0c1d *inst/extdata/LACHESIS_package_structure.png
94d2629d85dd4ad90b5186bc2a9f8f04 *inst/extdata/NBE11/NBE11_comb_pro_extra2.59_0.83.txt
f2c857419ed7f5dbbffb0d8bf49a3e66 *inst/extdata/NBE11/snvs_NBE11_somatic_snvs_conf_8_to_10.vcf
3fb79b6ea7c72d99a6f70a740c21897a *inst/extdata/NBE15/NBE15_comb_pro_extra2.51_1.txt
cab67f45f44823a375a6dc56fcc6ee09 *inst/extdata/NBE15/snvs_NBE15_somatic_snvs_conf_8_to_10.vcf
8c2861c8ba5fd9684ab865ff57b1a98c *inst/extdata/NBE15_Decomposed_MutationType_Probabilities.txt
797d549a3dbe3e849b6368f107642cd6 *inst/extdata/NBE26/NBE26_comb_pro_extra3.25_0.88.txt
c2404a7f1d0318ca172913d1e81038a0 *inst/extdata/NBE26/snvs_NBE26_somatic_snvs_conf_8_to_10.vcf
c512c56d132731f632c2eb60b9b77315 *inst/extdata/NBE63/NBE63_comb_pro_extra2.3_0.97.txt
a0cbbc83811d5f2f7f5fa3d605c9160f *inst/extdata/NBE63/snvs_NBE63_somatic_snvs_conf_8_to_10.vcf
cbe3b7e8f5b22a068a48b262a0b57b19 *inst/extdata/PURPLE/NB-S-599-T.purple.cnv.somatic.tsv
f4e1e6bf35e79c2e8526ff6ab3e8285d *inst/extdata/Sample_template.txt
e458dac4d633e7813bf0dc172e2d9c6a *inst/extdata/Sample_template.xlsx
1f9e529df8c9acdffd07bddf25f58c11 *inst/extdata/VAF_negative_example.png
8a03b871ab43dd81ac75e324e83be133 *inst/extdata/VAF_positive_example.png
f297b6b0a60ba50cff8b7b29e8822a8c *inst/extdata/cancerhotspots_v2_GRCh37_adapted.tsv
d27d41ecfcf573d40f07f0bc3578ccff *inst/extdata/cancerhotspots_v2_GRCh38_adapted.tsv
ea81f3887d05ae2971a537a5705968e7 *inst/extdata/mutect.somatic.vcf.gz
a099dd5544af73fcac562e530cfa78d0 *inst/extdata/mutect.somatic.vcf.gz.csi
12829bd76d98be37c3a2843c89c2b2f8 *inst/extdata/other.vcf
0176ae877742f09b2780db5bdba5134d *inst/extdata/strelka2.somatic.snvs.vcf.gz
f3936b51b11414d93b113331d4893ed5 *inst/extdata/strelka2.somatic.snvs.vcf.gz.csi
2f8f961f8ad62b115ba13dd38c8d198a *inst/intdata/hg19.sizes
83fb1c17d81cedfa9d5bbd663a09b4e2 *inst/intdata/mm10.sizes
645e86ccf2d7dabf731c1b3ec1552b7a *inst/tinytest/test_nbImport.R
1a431e20711554b480050e1b9de3951c *inst/tinytest/test_readCNV.R
2aba5ee4ea9e82469415a25c55803e2a *inst/tinytest/test_readVCF.R
dbf2f2a22b758a701919946a99a76163 *man/LACHESIS.Rd
eb2d7ce5ffa82c95af48b469104cfa7d *man/MRCA.Rd
a65380d058f62a0079e4f9566bbf315d *man/classifyLACHESIS.Rd
9b869552ed6762f13f8954fa24c490ec *man/clonalMutationCounter.Rd
3d5b872216e3ef4f3a9231b21c5bb9c7 *man/estimateClonality.Rd
a83ab9d604d3715d18a513d9fb4cbd97 *man/figures/LACHESIS_logo.svg
2e00bda4b6911ec7fa813933870f0cf1 *man/nbImport.Rd
ca0f3d0ecdd5f83632a577bf346bb232 *man/normalizeCounts.Rd
73da755bfaec5a1325406f9f51419b6c *man/plotClinicalCorrelations.Rd
91271229fbc0e363f0d89920d28298eb *man/plotClonality.Rd
259d17d3e3efd8987b02c5c41adc411a *man/plotDiseaseTrajectories.Rd
a4e10ea22967fd9b41f5c46b36a758b0 *man/plotLachesis.Rd
e112c020c332e290ec3aef614aec1269 *man/plotMutationDensities.Rd
94fb55957c06854a2e2f40dbc3e903ac *man/plotNB.Rd
ed5447c04c84be128b07b8bca304743d *man/plotSurvival.Rd
ad55f10eb96991d37028fa95dcd83b23 *man/plotVAFdistr.Rd
8d8ed85d0cfa5a33bee80a517c335b57 *man/readCNV.Rd
65103d54ef091c72f3796245e0ea11c5 *man/readVCF.Rd
e28227c2787f151dd97646d0a8453370 *tests/tinytest.R
e31c2b587f2dc3f27fbf83dc9eb7728b *tests/tinytest/test_examples.R
5fb830089453d73dc00343062462fa7f *tests/tinytest/test_integration.R
be3780a8b5882b5aa92cd63bd29ce2df *tests/tinytest/test_nbImport.R
ec778332106fc2467ef8cdfdfa060ac6 *tests/tinytest/test_parameter_validation.R
594690af484b31828bbd8064e9ea6d05 *tests/tinytest/test_readCNV.R
4d1e45df05491815d3495b22959b15f6 *tests/tinytest/test_readVCF.R
5387441838aff04468ce3042d65c107f *tests/tinytest/test_signature_assignment.R
2818e632df1c7c1b17db31c304c890dc *vignettes/vignette_LACHESIS.Rmd
