d207e3e77f73390142f674c9e70ffe31 *CITATION
3117737702dd77cca6751ad12a8d4b1c *DESCRIPTION
7ac254cc2c19ac7aa2d1952135f9d8f7 *INDEX
641ddd5e1c79ecc08913631fecc37231 *Meta/Rd.rds
f208ad11c6a68e75842aadf8a7b7e39b *Meta/data.rds
67d0d5964f3a04d88f780b55cff145de *Meta/features.rds
65961d75cb29565474a9637e14105592 *Meta/hsearch.rds
d1427ff32583d38b6063d154ce8b7989 *Meta/links.rds
93eec7507796e8f9cba30ca05f9b9385 *Meta/nsInfo.rds
8951e30ef497cf148ff7fa1e07c5990c *Meta/package.rds
6bb25cc454bbee77a164cfcf042fd286 *Meta/vignette.rds
487f5f5e09b11c376433ff2e93c0c3a8 *NAMESPACE
0ac63396a2f64dbcd1efed6a9c1676e1 *NEWS
ebf0fc819595d631b8bf280c4b049940 *R/PureCN
65688df9a66a1637b5886be2c9c92b28 *R/PureCN.rdb
d25af5a8335ac006c773bd04a6b6289d *R/PureCN.rdx
c0a1abec0c9afac63f2d710015c543f1 *data/centromeres.rda
346af3078a84dae224353d53bf1894d4 *data/datalist
3b43e27c728d8531b64372cc8960bbf1 *data/purecn.DNAcopy.bdry.rda
e5eec99c760102b6416b6461a49edffc *data/purecn.example.output.rda
c5de691084786f7909d37a4eaa34dce2 *doc/PureCN.R
eff40c91105089e0bbff232489bc27b3 *doc/PureCN.Rnw
5e45c14dd33120c098340635b8a2ab77 *doc/PureCN.pdf
1ae545918c436da92f18105464b0c593 *doc/Quick.R
bfcd0a964314946a7cd600399f9b021c *doc/Quick.Rnw
08237ac47cf2d1f710f49ac794cb3126 *doc/Quick.pdf
51a2335a5fe463776b4078e8a48c344a *doc/index.html
c49e37c5999315106b558210d3ba7b38 *extdata/Coverage.R
d6783d18995045bcc0cc5460f71fb498 *extdata/Dx.R
bffa45092fe60030c0ad54b62b510f99 *extdata/FilterCallableLoci.R
b24b32f79257168addfb9c1f8320a63c *extdata/IntervalFile.R
cd545c79e8d7ea766d4323182022d202 *extdata/NormalDB.R
de2ab5ff0e6c6f8c9d0fb2c4fdbdac7b *extdata/PureCN.R
dc147e94ae2855d472787c9ce77eb530 *extdata/dist/calculateSbdry.R
3e55f3cbacf0ade2c2a406f1ad3f51b7 *extdata/dist/downloadCentromeres.R
7df758adaaf5b6d487ac22e4dba6c31e *extdata/ex1.bam
1888862b9d22ddb8ca663eabc41c78f0 *extdata/ex1.bam.bai
7ff3a77a583973ad739082fc7d327298 *extdata/ex1_gcgene.txt
3cde10782966a832047779d3d1294e46 *extdata/ex1_intervals.txt
3600e3733184b2cf5822b61d26114658 *extdata/ex2_intervals.bed
ff600751c668406cf7c32e7362ce3899 *extdata/ex2_intervals.txt
3182e4f35fef60cd6a0d9fdec742c79b *extdata/ex2_mappability.bed
e77fc2dcfc240ed02caf5f6d8cce5559 *extdata/ex2_mappability.bigWig
fbe2d2fffd0dc64303686f11b5817883 *extdata/ex2_reference.fa
35fcb62fd46b593d1269e249174c30ff *extdata/ex2_reference.fa.fai
132903c9cf51362b793d719a82500098 *extdata/ex2_reptiming.bed
9b97a8416ce0918d993be657b41ef8b9 *extdata/ex3_intervals.bed
bad94524668ccd54248551b63caf6d41 *extdata/ex3_mappability.bed
559ee8cb44c6df4fe00696181ef07c60 *extdata/ex3_reference.fa
b9affa44c1486b4a1dfe8552bc60b25c *extdata/ex3_reference.fa.fai
9242303d61055871f27ea41c01c1db36 *extdata/example_callable.bed.gz
3b1ed770f9de08a67d73e260b6bc97af *extdata/example_cosmic.vcf.gz
cb4501c1bb40ad0b7af797f7a756d74e *extdata/example_cosmic.vcf.gz.tbi
7cf6ebfc8d897064bdcd935830ef708d *extdata/example_intervals.txt
91e6bf7827f9f6de08942bcd9456a321 *extdata/example_mutect2.vcf.gz
f5c82a061425aff64204e05b5720a226 *extdata/example_mutect2.vcf.gz.tbi
78d8aca0fe4427f63b85c6fdc3d9bdb6 *extdata/example_normal.list
a412992421727d291a7d65cc62cd5db8 *extdata/example_normal.txt
3b6c3ae906b6dd7c11f67e1713232926 *extdata/example_normal2.txt
15d982eb620d8f5cdf671c75d96b745d *extdata/example_normal3.cnn
9f8f7691886d943ef1e0e70ca00cabf0 *extdata/example_normal4.cnr
2a18a775c4d52d67095e83ffd9943f39 *extdata/example_normal5.hdf5
bb5da3767dabbd7a51ae717fddfef7d4 *extdata/example_seg.txt
ba6cdc51e670166d3932f7f66a3bc241 *extdata/example_single.vcf.gz
98d086d895796257dc4c6a312773e222 *extdata/example_single.vcf.gz.tbi
79937e90092e791bd91c7a045bd921e9 *extdata/example_tumor.txt
cfcfe0c54614686bd514ecafe41925c2 *extdata/example_vcf.vcf.gz
516302874424e3b8b8eaf5e45171da38 *extdata/example_vcf.vcf.gz.tbi
edf609a37d88244a6c43b8d7a4e86c27 *extdata/normalpanel.vcf.gz
d9676085e3af0a6e9847bf329e96e1be *extdata/normalpanel.vcf.gz.tbi
efc17f1901c0090230be09f42bd24366 *extdata/test_coverage_overlapping_intervals.txt
edb9079354f45e0fd7963c8ba1b4d2bb *help/AnIndex
ec927e466be47163d411f619983dfd0e *help/PureCN.rdb
ac68529d367b918f992c21436e38ef62 *help/PureCN.rdx
47a8caa80254727897d491e8b4175173 *help/aliases.rds
bb0ba4cacee8fd48439b74c8cc767f0d *help/paths.rds
fb7a97d0ca20a2ba0c5f19f82e94efdb *html/00Index.html
ef2537511c0bd1e2e8a7827858708400 *html/PureCN-defunct.html
3b01380d1784dff817358ba620a62d63 *html/PureCN-deprecated.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
c93c59013a0f69aa0e9c3861ef5ada9e *html/annotateTargets.html
6c038b52ffd75c99b5fa419d0290d3bb *html/bootstrapResults.html
3092fd0bce1ffc9fc2888917e41c919e *html/calculateBamCoverageByInterval.html
03fdc4df99355a0f742de18aa37d1b48 *html/calculateGCContentByInterval.html
c14967c55308bd6e463b5f6ecd89e516 *html/calculateLogRatio.html
6077b0bbbd98cd387bdbb0e446602eee *html/calculateMappingBiasVcf.html
bc1563d5b7caf3b213f9c56cc8d8709b *html/calculatePowerDetectSomatic.html
d86de2680c888a92e2e102fdc4c0d780 *html/calculateTangentNormal.html
8bb05798b02359ad7bcb42c6b8fde1b7 *html/callAlterations.html
56dd2577c6a800e7afd051b08cb1cf48 *html/callAlterationsFromSegmentation.html
49628a74a48b2292442a514920a80f21 *html/callLOH.html
623ebf230a720fe2e00fa75bffff2a35 *html/callMutationBurden.html
900f77b45bdab55d8b9d8588f0384a24 *html/centromeres.html
7f5ddec7bb216c25af0e795fe07cad16 *html/correctCoverageBias.html
fe9c25ffafe49388e6bde779893a13cb *html/createCurationFile.html
7c0868be8701fdec4c409e78f2b199eb *html/createNormalDatabase.html
d8441bb4610bf7860cb990450a78f2cf *html/createTargetWeights.html
f8ea1a7f365d872c99279077f2fc8793 *html/filterTargets.html
3ec80dfdacca5fe5107638ba88e83293 *html/filterVcfBasic.html
3024e4f1c25a9766eb5e4778f08b5126 *html/filterVcfMuTect.html
dffb55f10421daab74fe3b3bad10fa43 *html/filterVcfMuTect2.html
71010afd16db9a26e5469956eb489375 *html/findBestNormal.html
cc6a517506edadd00a9ddaf746dad5ea *html/findFocal.html
19ebe4c392741c6e596efdada389b164 *html/getSexFromCoverage.html
5cdfdc1230b92b6a7a3fe7815afd8418 *html/getSexFromVcf.html
6686144925f601e18b38f07bf1884fc7 *html/plotAbs.html
5d78aa87a35194b31a60b782ba25f11a *html/plotBestNormal.html
ea68d80fcc8943f4daa5b3e09982067c *html/poolCoverage.html
9c5011b8021a241eef21d7e1105c09b4 *html/predictSomatic.html
07b6b6b0f3e4fbd8fdb790c842b81313 *html/preprocessIntervals.html
e492c2d8fb2472ac96656330be701c6a *html/purecn.DNAcopy.bdry.html
ed23126e45d9e6f635f188b071973d92 *html/purecn.example.output.html
e6f5472e20075f8e57046d27232ca2dc *html/readCoverageFile.html
2f6087a03eb77caa88e52ce0ee4b9944 *html/readCurationFile.html
00417f04d34daca77f4fbfbd8bf6820e *html/runAbsoluteCN.html
71efbc305a28eb3675d69e4e55e3d366 *html/segmentationCBS.html
808a5af93f9d8bfdeb77213e789c9cfb *html/segmentationPSCBS.html
a5afdc83edddd9b8919849fdab723cd2 *html/setMappingBiasVcf.html
2da9ee9bff0f2fbb8743842d3b6cfa30 *html/setPriorVcf.html
